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Please accept my sincere apologies for the various mistakes and inaccuracies that escaped our attention. Fortunately only few true errors have been discovered so far. Some figures have been updated or improved and can be downloaded from this page.

Format: page, paragraph, line(S=sidebar C=figure caption, E=equation, B=Box, F=figure), minus means 'from bottom' Error description        (Submit a new one) Remarks Rev
Num		 Revision Status
for
e-print
After xiii, para2?? Acknowledgement for 2nd printing corrections here 1 Missing
Preface 1, 2, 11 an array of can be deleted can stay 2  
x, 1, 6 real (projections) of molecules should be projections of real molecules   3  
xi, 5, 6 broad and helpful should be large and helpful   4  
xii, 4, 1 the numerous should be all the   5  
xii, 5, 17 LBNL should be LANL Sorry, Tom. 6  
1, 1, 7 brief should be short   7  
3, S, col 2, line fig 13-23 c_hannel should be channel   8  
5, 2, 3 bad hyphenation, should be crystallo-graphy  or maybe not? 9  
5, 2,13 sensitive should be susceptible   10  
5,3,4 This not the should be This is not the Thanks, Boaz! 11  
7, 3, 5 may not locally represent the protein structure should be may not represent the local protein structure   12  
8, 3, 5 structures should be structure   13  
11, 1-2, break paragraph break to large   14  
13, 4, 10 cryocool should be cool   15  
19, S1-4, 13 new reference to PDBe should be added 1. Velankar S, Best C, Beuth B, et al. (2010) PDBe: Protein Data Bank in Europe. Nucl. Acids Res. 38, D308-D317. 16 ignored
20,4,11 graphic should be graphics   17  
  Chapter 2      
24,5,3 seleno cysteine should be selenocysteine check throughout chapter 2 18  
25, C2-1 add reference to 2009 Nobel Prize for Ribosome before "PDB entries..." For their work ultimately leading to the determination of the ribosome 50S subunit structure, V. Ramakrishnan, T. A. Steitz and A. E. Yonah shared the 2009 Nobel Prize in Chemistry.  19 year 2009 missing
26, C2-2,-2 David Stewart should be David Stuart Thx, Tomas! 19a NEW
27,1,1 deviate should be vary   20  
28,2,9 As most should be Because most   21  
29,2,2 delete 20   22  
29,2,3 The peptide bond is formed between two amino acids between should be The peptide bond between two amino acids is formed between   23  
31, C2-9, 9 cis should be italic cis   24  
31,2,6 described should be discussed   25  
33,S2-3, 1,13 of proteins should be in proteins   26  
35,C2-13 Add a remark that the PP-II helix is in the strict sense of backbone interactions not a bona fide SS element. ...nitrogen. A PP-II helix therefore does not not comply with the strict definition of secondary structure elements via their backbone hydrogen bonding patterns.   27  
35, 3,13 -180/+180 should be +180/+180 (the same but would be more consistent)   28  
36,2,10 the strands and extended should be the strands. Extended   29  
36,3,5 idealized should be ideal   30  
36,F2-14 The arrows in the right panel are inconsistent with chain direction updated figure for download (gif) here 31  
36,F2-14 Note to typesetter: figure 2-14 has been updated  - new fig (bmp) needs to be picked up from server - do not use old figure Thanks Tobias! 32 NOT BMP USED
39,2,8 So far, we have not needed to pay should be So far we did not have to pay ... 33  
40,1,9 amino acids and proteins should be amino acid residues in proteins.   34  
44,2,6 by surface should be via surface   35  
45,2,2 the rigid should be the rigidity of the   36  
46, F2-25 The side chain NH2CO should be flipped for consistency with density updated figure for download (gif) here 37 NOT BMP USED
  Note to typesetter: the figures listed to the right have been updated (color scheme of annotation) - new figs (bmp) need to be picked up from server - do not use old figures 2-20, 2-21, 2-22, 2-23, 2-24, 2-25, 2-26, 2-28 38 NOT USED-
MUST REPLACE!
46, C2-26, 1 S-S double bond should be S-S bond Thx, Manfred! 39  
47,3,3 chain density. should be chain.   40  
48,4,3 on surface accessible proteins should be on the surface of proteins. What was I thinking here.. 41  
52,2,5 receptor drug should be receptor-drug   42  
56,4,2 It is useful as it exemplifies should be It exemplifies   43  
56,c2-25, 1 and 3 motif serving should be motif (A) serving
domain of should be domain (B) of		 Insert figure labels in caption 44  
58,1,-1 Add to paragraph: A particularly efficient program for the detection of structural relationships across domain boundaries and under full consideration of biological unit information is implemented in the COPS server. xy Add reference xy - see page 76 45 IGNORED
62,1,1 As we discussed should be As discussed   46  
62,3,19 with crystal should be with the crystal   47  
62,3,21 task for should be task in the case of   48  
66,C2-43,3 and 9 purine bases are joined should be purin bases (A)are joined
form a nucleotide. should be form a nucleotide (B).		 Insert figure labels in caption 49  
68,C2-45,10 hydrogen donor should be hydrogen bond donor Thx, Manfred! 50  
68,C2-45,16 hydrogen acceptors should be hydrogen bond acceptors Thx, Manfred! 51  
68,C2-46,12 Zn atoms should be Zn2+ ions

ions not atoms		 Thx, Manfred! 52 INCORRECT CORRECTION
73, 2.12 Additional reading should include reference

1. Liljas A, Liljas L, Piskur J, et al. (2009) Textbook of Structural Biology. Hackensack, NJ: World Scientific Publishing Company.

 53 IGNORED
75 Update reference 50
50. Chen VB, Arendall WB, III, Headd JJ, et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66(1), 12-21. 54  
76 Add to references xy.  Suhrer SJ, Wiederstein M, Gruber M, et al. (2009) COPS - a novel workbench for explorations in fold space. Nucleic Acids Research 37(suppl 2), W539-W544. 55 IGNORED
  CHAPTER 3      
78,2,1 The following should be The remaining   56  
79,C 3-2,6 cheap and should be cheap, and   57  
80,2,8 In contrast, polycrystalline material contains a randomly oriented sample of many thousands of tiny microcrystals.. should be   In contrast, polycrystalline material contains many thousands of tiny, randomly oriented microcrystals..  58  
82, S3-3,5 just in crystals should be just as in crystals   59  
83,3,6 the limited power of global descriptors to pinpoint local properties. should be the insensitivity of global descriptors regarding local errors. 60  
86,3,3 < 95% should be > 95% Thx, Manfred! 61  
87,3,5 salt in should be salt-in inconsistent throughout text 62  
88,1,15 Finally, all kinds should be Finally, various kinds   64  
88,4,1 Once the activation barrier should be Once the kinetic barrier   64a NEW
89, F3-7 Note to typesetter: figure 3-7 has been updated  - new fig (bmp) needs to be picked up from server - do not use old figure Figure (gif) here - thx Julek! 65 WRONG IMAGE - NOT BMP
89, C3-7, -3 (often in the form of precipitate or should be (such as precipitate or   66  
89, 3, -6 advantage for one should be advantage of one   66a  NEW 
90,3,12 range 25-150 should be range of 25-150   67  
92,1,6 also, unfortunately, common protein-rich should be also, unfortunately common, protein-rich   68  
92,F3-9 Note to typesetter: figure 3-9 has been updated  - new fig (bmp) needs to be picked up from server - do not use old figure Figure (gif) here 69 WRONG IMAGE - NOT BMP
92, C3-9 Note to typestetter: use revised figure caption from server /chapter_3/caption_3-9.docx here 70  
93, S3-6, 1,6 Add reference xz: flow equation. should be flow equation.141  Reference xz: 141. Garcia-Ruiz J-M (2003) Nucleation of protein crystals. J. Struct. Biol. 142(1), 22-31. 70a REFERENCE 141 NOW
93, S3-6, 2,1 In Equation 3-4 should be In the Gibbs-Thompson expression 3-4 Thx, Wolfgang! 70b  
94,1,12 or for other kinetic reasons should be or for other, kinetic, reasons   71  
95,1,5 inspection. should be inspection of the diffraction pattern.   72  
95,2,2 where it reaches should be where the solution reaches   73  
96, 1, 4,5 Salting-in, salting-out need consistent hyphens  inconsistent throughout text 74  

96, E 3-5

Typesetting error, correct equation:

 formula 3-5

 75  
96,C3-13,-2 (salting in) and the salting out region should be (cation-dominated salting-in) and the anion-dominated salting out region   76  
97,2,4  Formula should be (H−(O−CH2−CH2)n−OH) Thx, Wolfgang! 76a  
97,2,5 Formula should be (H3C−(O−CH2−CH2)n−OH) Thx, Wolfgang! 76b  
97, 3, 1 (S) should be without parenthesis S   77  
98, 2, 1 magnitude should be multitude   78  
98, 4, 4 used should be useful   79  
101, 4, 1 is just to mix should be is to just mix   80  
104,4,1 paragraph should start with bold Clear drops.   81  
105, S3-10, -12 of 50 ml should be of 50 µl microliter 82  
105,2,2 directly to create should be to immediately create or instantaneously ? 83  
106,C3-34, add Add after last sentence: The shape of the solubility curve is typical for a salt-based precipitate cocktail (compare Figure 3-13); PEGs do not show a salting-in effect. Thx, Julek! 84  
108,C3-27, last Juan-Maria should be Juan-Manuel Sorry, J.-M.! 85  
111, 3, after last sentence after ...control experiments. , add: It has been proposed that the change in cocktail composition due to addition of seeds stock may also be a contributing factor towards increased crystallization successx, but recent studies remphasize the importance of an actual presence of nucleation sitesxx. References x, xx:

x. St John FJ, Feng B, & Pozharski E (2008) The role of bias in crystallization conditions in automated microseeding. Acta  Crystallogr. D64, 1222-1227.

xx. Shaw-Stewart PD, Kolek SA, Briggs RA, et al. (2011) The use of microseeding in protein crystallization: practical variations on the microseed matrix-screening (MMS) method. Acta Crystallogr. D67, in press.

 86 IGNORED
112, B 3-7, 1 any conditions should read the exact conditions   87  
113, S3-13, 9 aliquots followed by protein addition with a single needle dispenser suffices should be aliquots, followed by protein addition with a single needle dispenser, suffices 88  
114,2,9 drop the 'all'   89  
115, C3-34, 4 The large cube should be the larger, green cube   90  
115, last paragraph last paragraph Full factorial designs. The second sentence contains various mistakes and should be replaced as follows:

...factors.88 For a 2-level, 4-factor full factorial design, 16 experiments are required, and we can interpret our grid screen experiment (pH, PEG) as a simple 2-factor experiment with 6 (pH) and 4 (PEG concentration) levels resulting in 24 combinations. However... 

Thanks Wolfgang for pointing this out! 91  
117, C3-35, -3 toward soluble should be toward highly soluble   92  
120,3,10 drop the 'only'   93  
122 Add sidebar 3-13A - can be picked up from server sidebar_3_13A.docx or here 94 IGNORED
123,6,2 glossarize IC50 in this line and the definition of IC50 should go into Glossary -> half maximal inhibitory concentration (IC50)

A measure of the effectiveness of a compound or drug in inhibiting biological or biochemical function. Quantifies how much of a particular drug or inhibitor is needed to inhibit a given biological process (such as enzyme or receptor activity) by half.		 95 IGNORED
124,2,3 occupation should be occupancy   96  
124,2,5 occupanc should be occupancy   97  
124,C3-40,8 occupation should be occupancy   98  
127,1,3 the radical should be radical   99  
127,1,12 cooling also should be cooling   100  
131,2,3 mAbs should be mABs   101  
139, ref 87 Add issue number 254(23)   102  
139, refs 99-102 101 and 102 are identical to 99 and 100, respectively Needs complete renumbering of references in body text past 100 103 IGNORED
140 Add reference 141 (139 after repair, also correction in new S3-13A necessary). Note new references x, xx, xz 141. Luft JR, Furlani NM, NeMoyer RE, et al. (2010) Crystal cookery - using high-throughput technologies and the grocery store as a teaching tool. J. Appl. Crystallogr. 43(5), 1189-1207. 104 IGNORED
  Chapter 4      
148,C4-3,-3 as much as a single should be as little as a single   105  
154,3,-5 two times result - resulting needs rephrasing by native 106 IGNORED
154,S4-3,2 Targeted mutagenesis of should be Mutagenesis of specific   107  
157,1,2 PCR (using should be PCR (epPCR, using   108  
157,1,-4 mutation mutants should be mutation ... 109  
159, FC4-11,4 E. coli should be Y. pestis   110  
160,S4-4,14 tools in these bacteria is smaller. should be tools available for these bacteria is limited.   111  
162,1,3 BL843 should be B834   111b NEW
162,1,3

various codons or strains should be various codon-optimized strains or strains

   112  
162,2,4 up to 1/10 should be up to ten times ... 113  
167,5,3 the stationary Ni should be the Ni   114  
168,1,-4 plus should be with, parenthesis removed  with.....site flows   maybe.... 115  
170,C4-14,5 Aequoria victoria should be Aequorea victoria Thx, Wolfgang! 116  
171,3,5 BL843(DE3) should be B834(DE3) Thx, Wolfgang! 117  
171,3,-3 partial occupation should be partial substitution add residue substitution matrix in Appx 118  
177, 3, 3 Asn-X-Ser(Thr), while should be Asn-X-Ser(Thr), with X any non-proline residue, while   118a NEW
178, C4-20,9 (red circles mannose, blue squares N-acetyglucosamine) should be (open circles mannose, full squares N-acetyglucosamine; see additional reading reference 9 for the Oxford glycan symbol notation)   118b Mandatory
178, F4-20 Typesetter: new updated figure 4-20 (bmp) needs to be picked up from server - do not use old figure. new figure (gif) here 118c Mandatory
191, in Additional reading add reference no 9 9. Marino K, Bones J, Kattla JJ, et al. (2010) A systematic approach to protein glycosylation analysis: a path through the maze. Nat Chem Biol 6(10), 713-23. 118d Mandatory
191, in Additional reading add reference no 7

7. Aricescu AR, Assenberg R, Bill RM, et al. (2006) Eukaryotic expression: developments for structural proteomics. Acta Crystallogr. D62(10), 1114-1124.

 119  
191, in Additional reading add reference no 8 8. Walden H (2010) Selenium incorporation using recombinant techniques. Acta Crystallogr. D66(4), 352-357. 120  
193, refs 83 and 90 refs 83 and 90 de Marco are identical All refs in text past 83 need to be renumbered 121 IGNORED
  CHAPTER 5      
197,3,9 material properties should be materials   122  
197,3,11 prote_in should be protein   123  
201,3,4 In the should be In our   124  
203,F 5-7 Origin in left panel should not have a ' who put that in ? NOT in original figure - updated figure (gif) can be downloaded here 125 NOT THE  GIF FIGURE
  Typesetter: new updated figure 5-7 (bmp) needs to be picked up from server - do not use old figure.   126 THIS ONE!
203,2,1 paragraph should be headed by bold Limitations imposed on symmetry operations. In periodically...   127  
204,B5-3,6 all rotation should be all crystallographic rotation My mistake - rotation not rotations 128 MY ERROR
204,3,-3 cell constants should be cell parameters this is debatable, but serves consistency  129  
205,F5-10b Origin of cell should be moved to red dyad for both different cell and different origin updated figure 5-10_b (gif) can be downloaded here. 130 NOT GIF FIGURE
  Typesetter: new updated figure 5-10_b (bmp) needs to be picked up from server - do not use old figure. improved for clarity 131 THIS ONE!
206,3,9 case) one should be case) of one   132  
208,F5-15 Add the hexagonal unit cell in blue lines to emphasize the same unit cell volume and relation to asymmetric unit. updated figure 5-15 (gif) can be downloaded here. 133 NOT YET DONE!
  Typesetter: new updated figure 5-15 (bmp) needs to be picked up from server - do not use old figure. improved for clarity 134 THIS ONE!
208, C5-15,end Add: The blue outlined unit cells are equivalent in area (volume) and contents to the standard unit cell defined by the vectors a and b. there is nothing wrong as it is but I think this addendum makes it even clearer. 135  
209, C5-16,-2 the trigonal unit cell should be the equivalent trigonal unit cell as shown in blue in Figure 5-15   136  
213,S5-2,col1,-1 isolated \greekbeta-strand should be isolated greekbeta-structure   137  
213,S5-2,col2,2 this \greekbeta-strand is should be these \greekbeta-strands are   138  
213,C5-21,6 the \greekbeta-strand should be the \greekbeta-structure   139  
213,C5-21,7-8 this \greekbeta-strand should be these \greekbeta-strands   140  
213,1,1 "near" perfect should be near-perfect   141  
214,1,-1 the resulting should be the corresponding   142  
215,2,4 thrid vector c perpendicular should be third vector perpendicular Thx, Mamoru! 142c NEW MANDATORY
216, F5-26 wrong labelling needs replacement
Typesetter: new updated figure 5-26 (bmp) needs to be picked up from server - do not use old figure.		 Thx, John!

here		 142a NEW
MANDARORY
216, 5,4 Typesettting error; correct in MS
(3/4a 1/3b 1/2a) should be (3/4a 1/3b 1/2c)		 Thx, Mamoru! 142b NEW MANDATORY
216, second paragraph from bottom, -1 Sentence should end with thus (3  -1 -1). remove the 31bar1bar. 143  
222,F5-34 one visible line is drawn invisible updated figure 5-34 (gif) can be downloaded here. 144 NOT THE GIF
222,F5-34 Typesetter: new updated figure 5-34 (bmp) needs to be picked up from server - do not use old figure.   145 THIS ONE!
224,4,2 to operator should be to the trivial symbolic operator   146  
224,symbolic operators and matrix Both the symbolic operator (2) and the matrix R3 are mistyped.... updated operators and matrices can be downloaded here. Thx, Jonathan! 147  
225, C5-36, 8 two folds should be two 2-folds correct in MS 147a MANDATORY
228,4,-4 parallel but should be parrallel to but   148  
230,1,7 all m positions should be all M positions   149  
230,2,1 "positions" should be "Positions"   150  
230, operator 4. 4. should be 4. Copyediting error? - correct in original MS 151  
231,8,2 (3200/42000 PDB entries) should be replaced with (Figure 5-44)   152  
232,C5-42, end contacts. should be contacts of an individual molecule.   152  
233,1,-1,-2 P becomes b·γ(not a!) should be P becomes b·cosγ (not a!) Thx, Mamoru! 152a MANDATORY
233,C5-43,-2 The odd degree signs are rubbish (already squawked in proof). Should be -> become (b·cosγ, b·sinγ, 0) = b·(-0.5, 0.866, 0).   153  
233, E5-4 (5-4) should be
 		 X and x are swapped..darn 154  
235,1,3 equal. should be even.   155  
235, F5-44 Figure had duplicte axis labels updated figure 5-44 (gif) can be downloaded here. 156 NOT THE GIF
235, F5-44 Typesetter: new updated figure 5-44 (bmp) needs to be picked up from server - do not use old figure. Thx, Greg! 157 THIS ONE
236,1,1-2 remove the statements (+1 DoF of rotation) and (point group n22......rotation) The parentheses statements are confusing in absence of further explanation 158  
237, F5-46 Figure labels updated. Typesetter: new updated figures 5-46 (bmp) and 5-47 (bmp) need to be picked up from server from Feb 1, 2011 on - do not use old figure. Thx, John!
here		 158a NOT THE GIF -THE SERVER BMP
238,1,-1 (31). should be (3 1). needs a space 159a  
238,2,-3 Weiss indices (∞, ½) we obtain by either procedure Miller indices (0 2); for the blue set (3 0); and should be Weiss indices (½, ∞) we obtain by either procedure Miller indices (2 0); for the blue set (0 3); and Thx, Luc! 159b  
240, second bullet correct formula is: was correct in MS 160  
240, 2, 3 to the real space axes should be to the other real space axis clearer this way 161  
240,c5-49 Add to legend: Note that in the case of an orthogonal real lattice the direction of each reciprocal axis coincides with the direction of its corresponding real axis.    162  
243,2,3 around the origin should be moved between infinite) and of infinite) around the origin of 163  
243,3,3 interpretation of should be construction rules for   164  
246 Add to 5.7 Additional reading 7. Dauter Z, & Jaskolski M (2010) How to read (and understand) Volume A of International Tables for Crystallography: an introduction for nonspecialists. J. Appl. Crystallogr. 43(5), 1150-1171. 165  
  CHAPTER 6      
249,F6-2 add a logarithmic frequency axis (cf Atkins) updated figure 6-2 (gif) can be downloaded here. 166  
249,F6-2 Typesetter: new updated figure 6-2 (bmp) needs to be picked up from server - do not use old figure.   167 NOT THE GIF -THE SERVER BMP
249,B6-1,-3 diffraction X-rays should be diffraction of X-rays   168  
249,B6-1,-5 allows the use of the should be allows using the probably better? 169  
249,B6-1, second eqn. second equations for frequency ν needs to be inverted, should be ν = c/λ Thx Wolfgang! 170  
251,C6-3,-6 of electric should be of the electric Thx Wolfgang! 171  
252,2,-3 see)of should be see) of Thx Wolfgang! 172  
253,2,-1 Figure 6-6 should be Figure 6-5   173  
255,-2,2 though expansion should be through expansion Thx Wolfgang! 174  
255,last line photons gets should be photons get   175  
255,S6-3, above last equation in mathematics, should be in mathematics, the Euler Identity   176  
255, S6-3, last equation The Euler Identity has the wrong sign replace formula with correct one:
 Euler Identity  Thx, Robert!		 177  
256,F6-8 needs to be replaced with new figure 6-8
Typesetter: new updated figure 6-8 (bmp) needs to be picked up from server - do not use old figure.		 updated gif here
 178 NOT THE GIF -THE SERVER BMP
256,C6-8,4 incoming and scattered should be scattered and incoming   179  
256,c6-8,-5 place (top panel). should be place.   180  
256,C6-8, end add after end of caption: The reason for assigning the scattering angle units of 2θ becomes obvious once the diffraction of X-rays is interpreted as reflection on lattice planes (Figure 6-15).    181  
256,3,3 First, should be Either   182  
257,2,3 orbits should be orbitals Thx, Andy! 183  
257,F6-10 Typesetter: revert to original figure 6-10 (bmp) - pls do not change aspect ratio. Somehow the aspect ratio changed - atom is an ellipsoid. Download from gallery. 184 NOT THE GIF -THE SERVER BMP
258,F6-11 needs to be replaced with new figure 6-11
Typesetter: new updated figure 6-11 (bmp) needs to be picked up from server - do not use old figure.		 updated gif here   185 NOT THE GIF -THE SERVER BMP
258, E6-10 First parenthesis term (lambda*r*s0-lambda*r*s1) should be (lambda*r*s1-lambda*r*s0) Thx, Tomas! 185a NEW
258, C6-11 First parenthesis term (lambda*r*s0-lambda*r*s1) should be (lambda*r*s1-lambda*r*s0) Thx, Tomas! 185b NEW
259, e6-13 drop the FS  in the beginning gif here 186  
259,2,1 FS should be fS Thx, Andy! 187  
259,first bullet,1 FS should be fS Thx, Andy! 188  
259,first bullet,2 FS should be fS  Thx, Andy! 189  
259,first bullet,3 delete which is anotated as fS Thx, Andy! 190  
259,S6-4,-2 The exponent misses the B-factor, should be This was correct in MS and copyedits. Grrr... 191  
259, bullet 4 after atomic volume, the sentence should continue atomic volume, it is convenient to use the dimensions of [e-] for the atomic scattering factor. Its exact definition however is the ratio of the atom's scattering to the scattering for a free electron, and therefore it is strictly speaking a dimensionless factor or 'quantity of dimension one'.    A can of worms we do not want to open.... 192 IGNORED
260,3,3 cat ions should be cations Thx Wolfgang! 193  
263,5,-2 correlation should be relation   194  
264,c6-14,-6 Scattering should be The total scattering   195  
264,c6-14, end Add: In practice, the straight-ahead scattering at 2θ = 0º cannot be separated from the unscattered direct (incoming or primary) beam. Thx, Andy! 196  
265,s6-7,-5 complied should be compiled Thx, Andy! 197  
266, f6-14 needs to be replaced with new figure 6-14
Typesetter: new updated figure 6-14 (bmp) needs to be picked up from server - do not use old figure.		 updated gif here  198 NOT THE GIF -THE SERVER BMP
266,-1,-4 space As should be space. As Thx Wolfgang! 199  
269,C6-18,10 The diffraction patterns should be In the first four rows, the diffraction patterns   200  
273, S6-10, -4 (http://ice.chem.wisc.edu/catalogitems/ScienceKits.htm) should be either (http://ice.chem.wisc.edu/Catalog/SciKits.html) or (see link on the book web site) Thx, Luc! 200a  
273,c6-22,-5 zone or should be zone (cusp) or Thanks, AK! 201  
276,-3,-2 zero, they are real should be zero, their structure factors are real   202  
277,last line equation Square of sin misplaced, should be 203  
278, 4th equation on page closing parenthesis missing  download here. Thx, Wolfgang! 204  
280, E6-45 xj should be Xj  download here. Thx, Wolfgang! 205  
281,Table 6-3 The epsilon for general reflections should be 1 not zero download corrected table here 206  
282, E6-47,6-48 the four later capital greek psi are inconsistent in font with the body text and first 2 psi Typesetter: use same letters with same font type as in body text  download here. Thx, Wolfgang! 207 IGNORED - MUST FIX
283, E6-49 I think proportional is better than equal
 download here 208  
283, 4, last line before e6-51 becomes15 should be becomes15,16 Thanks, Kay and Jim! 209  
283, 7, last line before e6-52 given16 should be given14 Thanks, Kay and Jim! 210  
285,F6-29 Removed the stray 'plot area' at M-edges updated figure 6-29 (gif) can be downloaded here. 211 NOT THE GIF -THE SERVER BMP 
285,F6-29 Typesetter: new updated figure 6-29 (bmp) needs to be picked up from server - do not use old figure.   212 NOT THE GIF -THE SERVER BMP 
287,2,-1 Structure, or EXAFS spectrum. should be Structure (EXAFS) spectrum.   213  
290 Insert new Sidebar 6-11a, update all other sidebar numbers and references
Typesetter: Word doc Sidebar_6-11a.docx in /data/book/chapter_6 on server		 gif here. 214 IGNORED 
291,eqn6-60 blue plus/minus signs need to be swapped  download here. Thx, Wolfgang! 215  
291,S6-12,Col2,3 improved should be improve   216  
294,3,-1 no more than should be up to   217  
297, B6-12,4 resonance absorption should be absorption   218  
297,B6-12,9 Line break after pairs of reflection which should be pairs of reflections.   219  
297,B6-12,9 New paragraph Similarly, dispersive should be Dispersive   220  
299,3,-3 Ewald sphere should be resolution sphere   221  
299,4,4 delete by ignoring T typesetter 222  
299,4,8 after formulas, by ignoring the two operator should be by ignoring T the two operator   223  
300, Table 6-6 space group 180 is mistyped - should be P6222 not P62222 (was correct in MS)  Thx, Tommy! 224  
302,1,1 the anomalous should be the imaginary anomalous   225  
302,S6-13,col2,1 le(a)vus should be l(a)evus Thx, Wolfgang! 226  
304, F6-40 Figure 6-40 had a labelling error. Typesetter: new updated figure 6-40 (bmp) needs to be picked up from server  - do not use old figure. Thx, Bryan!
fixed gif here		 226a NOT THE GIF -THE SERVER BMP  
306,1,-1 delete last sentence They automatically....entire unit cell.   227  
311, ref 14 old reference 16 should become new reference 14 14. Giacovazzo C, Monaco HL, Viterbo D, et al. (2002) Fundamentals of Crystallography. Oxford, UK: Oxford Science Publications. 228  
311, ref 15 old reference 15 superceded by new reference, old ref 15 deleted 15. Milch JR, & Minor TC (1974) The indexing of single-crystal X-ray rotation photographs. J. Appl. Crystallogr. 7, 502-505. 229  
311, ref 16 old reference 14 should become new reference 16 16. Kabsch W (1988) Evaluation of single-crystal X-ray diffraction data from a position-sensitive detector. J. Appl. Crystallogr. 21, 916–924. 230  
311, ref 30 Methoda should be Methods was ok in MS and copyedits 231  
  CHAPTER 7       
313,1,4 the related concept should be the concept   231a IGNORED 
314, 5,2 data, should be data;   231b IGNORED  
314, 5,3 scaling, should be scaling;   213c IGNORED  
314,5,4 phasing, should be phasing;   213d IGNORED  
314,5,-3 and the related Bayesian should be and Bayesian   213e IGNORED  
314,B7-1,3 and related Bayesian should be and Bayesian   213f IGNORED  
315, C7-1, -9 variance σ2x , the should be variance σ2x (indicating the width of the distribution), the   213g IGNORED  
316, 3 lines after E7-4 individual probabilities should be individual (marginal) probabilities   213h IGNORED  
317,4 line from bottom then becomes should be then becomes the joint probability   213i IGNORED 
317, 2 line from bottom desired probability should be desired marginal probability   213j IGNORED 
318,2,1 variables should be variables (marginalization)   213k IGNORED  
318,6 line from bottom sometimes (for obvious reasons) should be sometimes   213l IGNORED  
319,1,3 Add: An exellent introduction to Probability and Bayesian Inference can be found in the highy recommended text by R. L. Winker (reference 6 in 7.13 Additional Reading).   213m IGNORED  
320, C7-2 Add: The Possion distribution itself is an limiting form of the Binomial distributon, given a large number of posssible independent events with a low probability of each to occur.   213n IGNORED  
320 I think a sidebar explaining the variance summations in bracket notation should go there.
Typesetter: Word doc Sidebar7-0.docx in /data/book/chapter_7 on server		 Image vailable here 232 IGNORED  
321, E7-24 replace formula with extended one 232b IGNORED  
321,C7-3,-4 after ...in its range. Insert following sentence ...in its range (the FWHM is often used to describe functions that do not have a defined variance, such as the Cauchy-Lorentz function in spectroscopy). The percentage....   234  
323, C7-5 Add: Because the CDF is obtained by integration of the underlying PDF, the slope (derivative) at a point of the CDF gives the value of the probability at that point. The figure verifies that the slope of the CDF is steepest at the peak of the PDF.     234a IGNORED  
324,4,-2 bative should be native   235  
324, C7-6, add add after last line of caption: We also realize that for a small number of samples (n < 10), the normal distribution underestimates the sampling error. In such cases, the t- or Student-distribution with its wider wings at small n is approriate for estimating the sampling error. For larger n, the Student distribution rapidly approaches the normal distribution.   235a IGNORED  
326, Eqn 7-35 Replace formula 7-35 with extended form 235b IGNORED  
327,last sentence o_r should be over   236  
329, E7-46 The outer parentheses are too fat typesetter 237 STILL ODD 
329, E7-47 The outer parentheses are too fat typesetter 238 STILL ODD 
330,S7-1,e2 for consistency 239 Superscript 2 too low 
330,2,2 of calculated structure factor amplitudes should be of structure factor amplitudes calculated   240  
332,6,2 R-value should be R-value   241  
335,1,1 provided 1763 should be provided in 1763 Thx, Shankar! 242  
335,1,2 centuries and should be centuries, and   243  
335, S7-2,1, 15  and function and even should be and function, and even Comma here for readability 244  
336, 5, 6 a proportionality constant should be a constant   244a IGNORED  
338,4,4 and for our should be and from our   245  
339,-2,2 just as a should be just a 9 lines up from bottom of page 246  
341,5, -5 observations xi should be observations xk Thx, Shankar! 247  
341,5, -4 variance σ2x(i) should be variance  σ2x(k) Thx, Shankar! 248 My Error
342,2,3 x, y, z, B, n and for each should be x, y, z, B, n for each   249  
342, paragraph after E7-82, 5 replace the formula - first derivative vector only, not second -correct in MS! 249b MANDATORY 
344,3,-2 thus intensities should be thus on intensities   250  
347,3,3 and the derived should be and the corresponding   250a IGNORED 
347,3,-1 model strucure factors. should be model structure.   250b IGNORED  
348, 2,-4 x follows the should be x is a   250c IGNORED  
348, eq 7-93b  outer parentheses humungous - was ok before New typesetting error  250d  NEW ERROR Mandatory 
348, last line distribution of atoms along the should be distribution of atom contributions along the   251  
349,4,1 the variance of /greeksigmaetc/ our should be the variance /greeksigmaetc/ of our   252  
349,6,1 (after E 7-98) coordinates y should be coordinates imply was correct in 2nd proof... 253  
350,C7-10,last statistical analysis. should be statistical descriptors.   254  
351,4,3 weak than general should be weak compared to general   254a MANDATORY
353,2,1 can be can be readily should be can be readily Thx, Shankar! 255  
353, eq 7-112  outer parentheses humungous - was ok before New typesetting error  255a  NEW ERROR Mandatory 
354, eq 7-114  outer parentheses humungous - was ok before New typesetting error  255b  NEW ERROR Mandatory 
354, E7-116 P(Z) should be N(Z):     256  
356,E7-118, E7-119 The large parentheses are too fat New typesetting error 257 WORSE NOW 
356,3,1 (line 18)  <Iobs>bin should be <Iabs>bin was correct in manuscript -thx Pete! 258  
356,6,1 Let us inspect should be Let us examine   259  
357,C7-15,6 regression though should be regression through   260  
358,-2,-5 Rice distribution. 46 known in should be Rice distribution 46 known in no period 260a  
361,1,7 imaginary parts should be imaginary axes   261  
361,C7-18,7 d · F should be d · f   262  
362,3,2 then needs should be needs   263  
363, E7-146 Equation mistyped Thanks, Robert! 263a Mandatory 
363, last para, last line  Woolfson distributions should be Woolfson amplitude distributions     263b  NEW 
368, 7.13 Add reference to Additional Reading 5. Jeffreys H (1973) Scientific Inference. Cambridge: Cambridge University Press. 263b Mandatory 
368, 7.13 Add reference to Additional Reading 6. Winkler RL (2010) An Introduction to Bayesian Inference and Decision. Gainesville, FL: Probabilistic Publishing. 263c Mandatory 
  CHAPTER 8       
372, T8-1 Capt, Line 1 Shorter wavelengths provide stronger diffraction but also higher absorption. should be X-rays with longer wavelengths (lower photon energy) provide stronger diffraction (Equation 6-52) but experience higher absorption (Figure 6-29 and Sidebar 6-11). Thx, Mamoru! 263d NEW, mandatoy
377,1,1 the solution of should be the solutions of   264  
377,1,7 They main should be The main Thx, Shankar! 265  
377, 2,6 named because cause should be named because Thx, Shankar! 266  
378,3,4 though a high should be through a high   267  
378,5,-5 the dispersive should be the anomalous and dispersive   268 IGNORED 
380,1,1 Huu at the University of California appears yellow highlighted No highlight 269  
380, C8-7 All my copies have a blue line/smudge in the caption Production check 270  
381,3,-3 can be can be should be can be Thx, Shankar! 271  
381, S8-2 Replace sidebar with updated sidebar sidebar_8_2_new.docx on server image here 272  
383,S8-3,4 1960s and the should be 1960s. The break sentence 273  
386, F8-13 replace figure 8-13 with updated figure with different loop. Replace last sentence of C8-13 New figure availabe here and in gallery 274  
  Typesetter: new updated figure 8-13 (bmp) needs to be picked up from server - do not use old figure. Production check, update 275 NOT THE GIF -THE SERVER BMP   
386, C8-13 Replace last sentence: ...mounting pin. The insert shows a harvested crystal in an older style nylon loop that is quite large for the crystal. Pre-fabricated loops are now availabe in many sizes, allowing to select a harvesting loop that matches crystal dimensions. The cross-hairs indicate the crystal location determined by image recognition software. Insert image courtesy of Andrea Schmidt, EMBL Hamburg. Thanks for the new insert, Andrea! 276  
385,2,8 with card or should be with a card or   277  
386,2,4 puck or a vial located in the puck (Figure 8-14). should be puck (Figure 8-14) or a vial located in the puck.   278  
390,C8-18,6 twin fraction α = 0.5 generates should be twin fraction α ≠ 0.5 generates was correct in manuscript -thx Shankar! 279  
390,C8-18,-3 with α ≠ 0.5, the should be with α = 0.5, the   280  
391, Table 8-3, trigonal The correct space groups for point groups 312 and 321 respectively are:
312    P312, P3112, P3212
321    P321, P3121, P3221		 Thx, Roberto! 280a MANDATORY 
394,3,-4 SHELXL and PHENIX/Refine should be SHELXL, REFMAC, and PHENIX/Refine update 281  
395,3,7 to abandon should be or to abandon   282  
396,3,4 latice should be lattice   283  
400,1,-1 only because should be because   284  
403,2,-2 of crystal should be of a crystal   285  
406,4,-2 capable of processing and refining modulated structures should be capable of processing incommensurate diffraction data and refining modulated structures   286 MANDATORY 
407,2,-6 advantage the should be advantage of the Thx, Shankar! 287  
409,2,-5 Wang should be B. C. Wang   288  
413, E 8-18  parentheses humungous - was ok before New typesetting error  288a  NEW ERROR Mandatory 
413,4-2 perferablycollected should be preferably collected   289  
416,B8-10, -1 Formula should be typeset like 8-24 typesetter error - was correct in proofs 290  
418,1,5 opposed should be related   291  
419,2,-2 which tends overall to result in worse should be which results in worse overall   292  
419,3,9 low penalty the should be low penalty. The   293  
419,3,-4 symmetry).  should be symmetry. 294  
422,T8-5; 423, T8-6 Does the highlighting in the table have to look this ugly? Revert to my original design. 295  
423,2,-3 (3.8%) should be (3.5%) Thx, Shankar! 296  
428,C8-42,3 The probability distribution plot (CDF, left panel) should be The plot of the cumulative probability distribution function (CDF, left panel)   297 My Error 
434, Additional Reading Add ref 9 to additional reading 9. Garman EF, Pearson AR, & Vonrhein C (2010) Experimental Phasing and Radiation Damage - Proceedings of the CCP4 study weekend. Acta Crystallogr. D66(4), 325-501. 298  
434, Additional Reading Add ref 10 to additional reading 10. Garman E (2010) Radiation damage in macromolecular crystallography: what is it and why should we care? Acta Crystallogr. D66(4), 339-351. 299  
Caption 8.9 8.9 References is misplaced in my pdf  typesetting error    NEW 
435, ref 38 Incorrect reference 38 38. Viola R, Carman P, Walsh J, et al. (2007) Automated robotic harvesting of protein crystals - addressing a critical bottleneck or instrumentation overkill? J. Struct. Funct. Genomics 8(4), 145-152. 299a  
  CHAPTER 9       
439, Figure The figure is too small.   300 IGNORED 
441,E9-7 The equation is typeset larger than others. Match typesetting 301  
442, e9-14 The equation is mistyped. it should be
 Hires jpg here
Thx, Tobias!		 302 DOT does not seem to be mathdot, different font size (cf 9-13) 
  On page 444 and 445 there are a series of correlated errors, resulting from the fact that I wrote 'convolution' several times when it should have been 'sampling'. The fact is that the diffraction pattern is of course the sampling (multiplication) of the molecular transform with the reciprocal lattice function, not convolution. This is correct in other places but I missed it here. Thanks, Erhard!

 303  
444, F9-2 convolution sign in lower panel should be multiplication symbol updated figure 9-2 (gif) can be downloaded here. 304  
444, F9-2 Note to typesetter: figure 9-2 has been updated  - new fig (bmp) needs to be picked up from server - do not use old figure   305 NOT THE GIF -THE SERVER BMP 
444,1,4 convolution should be sampling (or multiplication)   306  
444,C9-2,7

as a convolution of the reciprocal lattice with the reciprocal transform of the molecule. should be as a sampling (multiplication) of the molecular transform with the reciprocal lattice.

  307  
444,C9-2,-1 delete corresponding   308  
445,1,2 Similarly, the sampling should be For their transforms, the sampling (or multiplication)   309  
445,1,4 to sampling should be to convoluting   310  
445,B9-2,-3 molecular envelope should be molecular scattering envelope   311  
447,S9-2,6 Friedels law should be Friedel's law   312  
447,S9-2,col2,8 or in practice compute should be or compute update 313  
447,S9-2, end Add: Some refinement programs such as REFMAC and SHELXL allow refinement against anomalous data. update 314  
448,Paragraph 1 Paragraph should be lead by Data truncation.   315  
448,Paragraph 2 Paragraph should be lead by Grid spacing.   316  
449,C9-6,5 occupation should be occupancy   317  
450, E9-21 rho(r\sub\j) should be rho(r\sub\i)
318  
451,C9-7,11 hydrophobic Ile should be hydrophobic Val .. 319  
452,1,3 molecules is should be molecules from electron density alone is   320  
453,s9-4, 1 The N in Nominal should not be blue highlighted but bold Thx, Shankar! 321  
454,C9-10,8 compete data should be complete data Thx, Shankar! 322  
454,C9-10,-7 missing at should be missing, but at   323  
455,1,2 Figure 9-11 the should be Figure 9-11, the   324  
455, C9-12 last character should be a l (use a serif font) - looks like a backslash   325  
456,3,-6 or B-factors, We should be or B-factors. We Thx, Shankar! 326  
457,1,1 same effect should be same attenuating effect   327  
457,1,2 B-factors and should be B-factors, and   328  
457,1,3 B-factor should be B-factor,   329  
459,3,3 phase error should be mean phase error   330  
461,S9-5, equation 4 r.m.s.(F, p_hs) should be r.m.s.(F, phs) Thx, Shankar! 331  
461,C9-18,-3 lower left should be lower right   332  
462,S9-6,4 or served should be or have served I think so.. 333  
463,lastpara,2 or finding should be or for finding I think so.. 334  
467,last para, last line Add sentence: Considering the centrosymmetry, the Patterson map has N(N-1)/2 unique peaks.   335  
  CHAPTER 10       
477,B10-1,1 The full stop after phasing. is blue Thx, Shankar! 336  
479,1,1 FPA for each derivative should be FP for the native   337  
479,B10-2,last sentence replace with: As a result of the weaker signal, anomalous phasing requires slightly more marker atoms per residue, but even....   338  
481,1,1 electronic should be scattering   339  
481,2,-4 Update reference 21
the emerging PHENIX21 suite should be the PHENIX21 suite 		21. Adams PD, Afonine PV, Bunkoczi G, et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallographica D66(2), 213-221. 340  
482,1,-5 possible metal should be possible   341  
484 last para,-3 R-value should be RF-value   342  
486 F10-11 parentheses too fat typesetter 343 Still?? 
487,1,3 1-1, 2-2, 3-3, 1-2, 1-3, and 2-3 should be 1-2, 1-3, 2-3, 2-1, 3-1 and 3-2   344  
493,3,4 heavy atom searches. should be more complex heavy atom searches.   345  
500,S10-3,5 described below. It was should be described in Section 10.7. CF was   346  
502,3,1 replace entire paragraph 'A single source ...Chapter 6' with Anomalous scattering of X-rays by heavy marker atoms can also provide a source of electronic differences. The result are intensity differences between two reflections of a Bijvoet pair, and the corresponding set of SAD data collected from a single crystal at a wavelength corresponding to a X-ray energy above an absorption edge will contain pairs of reflections with different intensities for non-phase-restricted reflections (compare the anomalous structure factor table computed for BPTI in Chapter 6).
  347 mandatory! 
502,5,2 anomalous contribution of an anomalous scatterer is should be anomalous scattering contribution f" is .. 348 double prime symbol sucks 
504,S10-4,col1,10 rapid should be fast   349  
504,S10-4,col1,-2 A version of SHELXE to be released soon119 will also include......module. should be SHELXE now also includes......module.119 see update ref 119 on page 545 350  
504,S10-4,col2,4 ....refinement.119 should be refinement (Sidebar 10-12). new sidebar 10-12 on page 535 351 NO NEW SIDEBAR 10-12 
504,S10-4,col2,2 will then provide should be provides update 352  
505,3,-4 pair such should be pair (such Thx, Shankar! 353  
507,2,-3 phase angles should be phase angle distribution   354  
507,T10-2,3 replacement and should be replacement, and   355  
511,1,5 map: the should be map. The   356  
511,1,-1 amplitude should be amplitude:   357  
519,6.line from bottom addition of should be summation of   358  
520,1,4

prob(Fi|FT, Hi)_ . should be prob(Fi|FT, Hi). (no space)
Thx, Shankar! 359  
522,2,1 produces aFourier should be produces Fourier Thx, Shankar! 360  
523,3, add At the end of paragraph, add: Bar charts showing the relative magnitude of HL-coefficients for various phasing scenarios can be found in the review by McCoy and Readx. x. McCoy AJ, & Read RJ (2010) Experimental phasing: best practice and pitfalls. Acta Crystallogr. D66(4), 458-469. 361 IGNORED 
526, S10-10,5 phasing method that should be phasing method (ARCIMBOLDO) that is   362  
526, 2, 7 g(x)-gas should be g(x)-g as (space before as missing)   363  
527,C10-26,10 near-random phase should be near-random mean phase   364  
530,3,-3 resolution and we check should be resolution. We therefore check   365  
531,5,-2 still can find should be still find Thx, Shankar! 366  
535, 1,4 add to paragraph: The switch -an used in the example below instructs SHELXE to conduct  n cycles of autotracing, with -nm specifying the number of NCS related copies in the asymmetric unit. Both switches are availabe in the most recent SHELXE release. -a in Courier-style fixed font
-n in Courier-style fixed font		 367  
535, 2,3 shelxd vta1_ fa
shelxc vta1 vta1_ fa –s0.5 –m20 –e1.0 –h -b
should be
shelxd vta1_fa
shelxe vta1 vta1_fa –s0.5 –m20 –e1.0 –h -b -a3  -n2		 correct in MS...remove also the spaces in vta1_ fa to vta1_fa

All in Courier-style fixed font		 368  
535, 3,1 with the input to SHELXD
should be
with the input to SHELXC (also including instructions used by SHELXD)		   369  
535,last para, -3 The returned model should be The model returned by the ARP/wARP server   370  
535,last para, -2 subunits should be copies   371  
535, last para Add: We could also have used the SHELXE poly-alanine model directly and rebuilt it with a model building program of our choice - an excellent exercise for beginners.   372 IGNORED 
535 add new sidebar 10-12
Typesetter: Word doc Sidebar10-12.docx in /data/book/chapter_12 on server		 image here 373 NO NEW SIDEBAR 
537,2,-5 f", and .... should be f". delete rest of garbled sentence. 374 MANDATORY 
538, C10-37, 9 edge is also an should be edge is an   375  
538,3,1 of the MAD should be of our MAD   376  
538,3,5 structures and should be structures, and   377  
542, Additional Reading Add ref 9 to additional reading 9. Garman EF, Pearson AR, & Vonrhein C (2010) Experimental Phasing and Radiation Damage - Proceedings of the CCP4 study weekend. Acta Crystallogr. D66(4), 325-501. 378  
542, Additional Reading Add ref 10 to additional reading 10. McCoy AJ, & Read RJ (2010) Experimental phasing: best practice and pitfalls. Acta Crystallogr. D66(4), 458-469. 379  
545, ref 119 update ref 119 119. Sheldrick GM (2010) Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr. D66, 479-485. 380  
545, ref 120 update reference 120 Nature Methods 6(9): 651-653 (2009) 381  
  CHAPTER 11       
547,1,4 associated should be corresponding   382  
547,4,2 crystal structure. should be crystal structure, given only diffraction data.    383  
550, t11-1, caption better than average should be better-than-average hyphens increase readability 384  
551,1,-6 structur-ally odd hyphenation 385  
551,1,-5 pairs LV and HV and LC and HC are should be pairs LV and HV, and LC and HC, are    386 Commas poorly spaced 
551,2,-2 symmetry, any should be symmetry, and any   387  
552,1,-4 The rotationn R  T. should beeThe rotationn Rtakes place around the center of mass of the molecule, followed by a translationn T. Was correct in MS - thx, Shankar! 388  
552, entire page All RA,B and TA,B - also in equations - should be replaced with RAB and TAB for consistent notation Figure 11-3 should be replaced, jpeg available here. 389  
  Note to typesetter: figure 11-3 has been updated  - new fig (bmp) needs to be picked up from server - do not use old figure   390 NOT THE GIF -THE SERVER BMP 
555, last para, -3 } The eigenvector should be }. The Eigenvector (full stop missing) Thx, Shankar! 391  
556,E11-14 for consistency all Ri,j should be Rij 392  
556,E11-15 for consistency all rij should be Rij 393  
556,paragraph Spherical Coordinates the capital greek symbols for phi Φ and psi Ψ in the paragraph text need to be replaced with small greek phi φ and psi ψ in this paragraph and in box 11-3. See formula 11-16 for correct symbols. Was correct in MS. 394  
556, C11-5,4 the lateral angle Φ should be the azimuthal angle φ (note correct smalll greek symbol phi) Thx, Shankar! 395  
556, C11-5,5 the azimuthal angle Ψ should be the lateral (inclination) angle ψ  (note correct smalll greek symbol psi)   396  
557,E11-16 for consistency all Ri,j should be Rij 397  
557,2,6 crystal. Rotations should be crystal lattice. Crystallographic rotations   398  
562,C11-8,6 of reflections similar should be of reflections, similar   399  
565,S11-2,last sentence boundaries. should be boundaries, or in the case of domain swapping.   400  
568,3,1 function G.. should be function G. Thx, Shankar! 401  
570,C11-16,3 NCS peak.. should be NCS peak. Thx, Shankar! 402  
573,3,4 difference should be experimental isomorphous or anomalous difference   403  
576,2,3 six parameters should be six placement parameters   404  
578,S115,Col2,9 largely sheet should be largely-sheet   405  
578,S115,Col2,11 largely helical should be largely-helical   406  
578,1,7 as a consequence many trials to find should be as a consequence, many trials are required to find   407 delete 'necessary'
582,C11-24, -3 crystallography symmetry should be crystallographic symmetry   408  
584,3,4 on a general position should be on a special position   409  
586,4,4 of oriented probe observed data. should be of the oriented probe and the observed data. ... 410  
592,C11-27,4 and not solvent should be (instead of solvent)   411  
594, S11-8 Add after last line: Following a thorough investigation, it has been determined that twelve structures reported by the same individual are based on fabricated data, and removal of these entires from the PDB has been recommended.114   Ref 114 on p 605 412  
596,C11-26,-2 Rice function and for centrics by the Woolfson function. should be Rice distribution and for centrics by the Woolfson distribution. 413  
598,F11-30 move figure and caption to top of page. typesetter 414  
598,E11-58 Brackets too fat, obscure superscript typesetter 415  
603 Update reference 9
9. Adams PD, Afonine PV, Bunkoczi G, et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallographica D66(2), 213-221. 416  
605,references Add reference 114 114. Baker EN, Dauter Z, Einspahr H, et al. (2010) In defence of our science - validation now! Acta Crystallogr. D66(2), 115. 417  
  CHAPTER 12       
607,1,2 model and local real space fitting of residues in electron density should be model into electron density and local real space fitting of residues   418  
607,3,1 errors remaining after rebuilding the model should be errors that remain after rebuilding, the model   419  
613,5,-5 60% should be 60°   420  
615,3,2 data and is should be data. L is   421  
619, B12-3, 1, 4 exp(φ) should be exp (i.φ) 2 times in in-line formulas, correct in manuscript! 421a NEW
619, B12-3, 2, 5 exp(φ) should be exp (i.φ) in FML formula, correct in manuscript! 421b NEW
622,1,2 delete  that need adjustment   422 New fix of fix 
622, B12-4, -6 for errors should be for non-random errors   423  
626,1,2 an a posteriori R-free can should be an a posteriori R-free 35 can Thx, Tommy! 424  
630,3,1 The phenyl and indolyl rings of Phe, Tyr, His, and Trp should be The phenyl, indole, and imidazole rings of Phe, Tyr, His, and Trp Thx, Tommy! 425  
631, C 12-13 Following a suggestion of George Sheldrick, add following paragraph after last sentence of figure caption: Note that different programs may use different definitions and atom naming conventions in their chiral volume calcuation. SHELXL for example uses ASCII-alphabetic order of the atom names, and assigns positive chiral volumes for the L-amino acids. In the REFMAC/PHENIX monomer library the sign of the chiral volume is explicitly assigned for each atom, and with ligand order N CB C it is always negative for CA. If Cahn-Ingold-Prelog priority rules for absolute configuration (Sidebar 6-13) were strictly applied, cysteine would have R-configuration, all other chiral common amino acids would have S-configuration.   426  
634,5,4 as restraint should be as a restraint   427  
635,S12-5,col2,3,-1 very computer intensive should be computationally intensive   428  
635,S12-5,col2,last paragraph line 4 refinement. should be refinement against anomalous data.   429 missing 
636,1,4 delete: the left panel of   430  
637,2,1 coordinates and should be coordinates, and   431  
637,2,last 2 sentences swap the last two sentences   432  
640, 3,-3 goodness-of-fit based should be goodness-of-fit   433  
640,last line of body text displacement vector should be displacement   434  
643, end of C12-16 add following: Note that in non-orthogonal crystal systems the always orthogonal truncation ellipsoid principal axes do not correspond directly to reciprocal axes. From the TRUNCATE manual: Direction 2 = b*; direction 3 = perpendicular to

a* and b*; direction 1 = perpendicular to b* and direction 3.

Thx Matthias for that comment! 435  
644,2,4 was deduced to should be was used to   436  
647,3,-1 delete: unnecessarily   437  
650,line after e12-87 Hessian matrix is Nabla squared: Correct in manuscript... 438  
650, above last line p0-p1 should be p-p1 needs to be checked 439  
653,S12-7,4 diffraction and should be diffraction, and   440  
657,1,3 procedure should be program   441  
657,1,4 and is should be and it is   442  
662, bullet2, -2 necessary benefit should be necessary requirement or just necessity Copyeditor to decide 443  
663, bullet5, 3 not simply a should be not just a   444  
667,3,5 which snap should be which then snap   445  
670 1,-1 compensating for should be absorbing   446  
670, C12-30, -5 2nls should be 1nls Thx, Kay and Pete! 447  
672,2,1 do have incorrectly should be do not have correctly   448  
683,1,4 1/1000 should be 1/10000   449  
689 Update reference 28 28. Emsley P, Lohkamp B, Scott WG, et al. (2010) Features and development of Coot. Acta Crystallogr. D66(4), 486-501. 450  
689 Correct reference 35 35. Kleywegt GJ, & Brunger AT (1996) Checking your imagination: applications of the free R value. Structure 4, 897-904. 451  
691 Update reference 133
133. Chen VB, Arendall WB, III, Headd JJ, et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66(1), 12-21. 452  
  CHAPTER 13      
695,3,-4 R-factor should be R-value that sucker slipped through.... 454  
701, T 13-2, lower header line deviatiom should be deviation Table and figure were correct in MS! 455  
707,2,first bullet,2 effect of a well-built or incorrect ligand should be effect of either a well-built or an incorrectly built ligand    456  
709,3,2 known and should be known ligands and   457  
711,S13-4,21 density and should be density, and   458  
711,C13-11,2 low affinity should be low-affinity   459  
711, F13-11 relabelled low-affinity, drug-like updated figure 13-11 (gif) can be downloaded here. 460  
  Typesetter: new updated figure 13-11 (bmp) needs to be picked up from server - do not use old figure.   461 NOT THE GIF -THE SERVER BMP 
711, last paragraph there is a blue smudge in my copies across the last 3 lines typesetter 462  
719,S13-6,col2,1 and B-correction should be and (negative) B-correction   463  
729,1,2 made) and should be made), and   464  
733 Add to 13.12 Additional reading 6. Rupp B (2010) Scientific inquiry, inference and critical reasoning in the macromolecular crystallography curriculum. J. Appl. Crystallogr. 43(5), 1242-1249. 465  
733 Update reference 21
 21. Chen VB, Arendall WB, III, Headd JJ, et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66(1), 12-21. 466  
  APPENDIX       
741 line after Eqn A-12 its elements should be its diagonal elements   467  
749,1,EQ A-54 Formula is wrong - delete norm bars and correct .... thanks, Ian, Dirk and Pavel! 468  
749,C A-1 Formula is wrong - delete norm bars and correct 469  
749, Paragraph below A-55 follows what is considered should be follows the Euler Identity, considered   470  
749, A-56 Euler Identity has wrong sign... correct: Euler Identity 471  
750,3 lines below Eqn A-67 \greekpsir should be \greekphir 472  
754,Table A-6 in Coulomb row, units are missing: 1 C         and       1 A·s 473 mathdot missing 
788,middle of page margin there are pink smudges in my copies ?? 474

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