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Table 1 Data collection and refinement statistics

From: Structure of the stationary phase survival protein YuiC from B.subtilis

Crystal +NAG (truncated K32-E218) Apo (P73-E218) +anhydro (R52-K217)
PDB CODE 4WJT 4WLI 4WLK
Data collection    
Wavelength (Å) 0.9795 0.9200 0.9795
Space group R3:H (146) (Hexagonal Cell) C2221 (20) R3:H (146) (Hexagonal Cell)
Cell dimensions    
a, b, c (Å) 145.5, 145.5, 37.8 50.0, 117.3, 61.0 147.2, 147.2, 37.9
 α, β, γ (°) 90, 90, 120 90, 90, 90 90, 90, 120
Resolution (Å)a 36.37–1.21 (1.23–1.21) 30.8–1.76 (1.79–1.76) 42.50–2.03 (2.08–2.03)
Total number of reflections a 290513 (14071) 132867 (7892) 74023 (5113)
Number of unique reflections a 89967 (4420) 18150 (1026) 19631 (1439)
Rmerge a 0.043 (0.569) 0.098 (0.745) 0.122 (0.576)
Rmeas a 0.060 (0.792) 0.114 (0.860) 0.162 (0.764)
Rpim a 0.041 (0.549) 0.057 (0.425) 0.106 (0.497)
CC (1/2) a 0.998 (0.607) 0.998 (0.771) 0.983 (0.620)
Solvent content (%) 45.7 53.3 44.0
Molecule/asymmetric unit 2 1 2
Wilson B-factor (Å2) 14.4 17.3 21.4
I/σI a 10.3 (2.4) 13 (2.5) 7.5 (2.2)
Completeness (%)a 98.8 (97.2) 99.8 (99.6) 99.4 (98.7)
Redundancy a 3.2 (3.2) 7.3 (7.7) 3.8 (3.6)
Refinement    
Resolution (Å)a 36.39–1.21 (1.23–1.21) 30.798–1.76 (1.85–1.76) 42.51–2.03 (2.14–2.03)
Reflection, working 85213 18131 19628
Reflection, free 4468 927 968
Rwork/Rfree (%) 11.1/14.4 16.2/20.2 16.76/20.80
No of non-H atoms 2815 1264 2506
 Protein A: 1185 B: 1185 1120 A: 1139 B: 1133
 Others 45 (NAG) 16 (EDO) 56 (1,6-anhydro-disaccharide)
  13 (Polypropylene glycol)   
  16 (DMSO)   
 Water 371 128 178
B factors (Å2)b 24.0 26.6 32.4
 Protein A: 21.7 B: 21.6 25.5 A: 33.1 B: 31.2
 Others 20.3 (NAG) 35.1 (EDO) 28.0 (1,6-anhydro-disaccharide)
  44.5 (Polypropylene glycol)   
  64.6 (DMSO)   
 Water 37.0 35.05 36.839
Rmsds    
 Bond lengths (Å) 0.023 0.016 0.005
 Bond angles (°) 2.2 1.495 0.990
Ramachandran plot    
 Favoured (%) 98.1 97.8 95.4
 Allowed (%) 1.8 2.4 4.6
 Outliers (%) 0 0 0
  1. a Values in parentheses are for the highest-resolution shell
  2. b Average over all atoms
  3. \( {R}_{merge}=\frac{{\displaystyle {\sum}_{hkl}}{\displaystyle {\sum}_j}\left|{I}_{hkl,j}-\left\langle {I}_{hkl}\right\rangle \right|}{{\displaystyle {\sum}_{hkl}}{\displaystyle {\sum}_j}{I}_{hkl,j}} \)
  4. \( {R}_{meas}=\frac{{\displaystyle {\sum}_{hkl}}\sqrt{\frac{n}{n-1}}{\displaystyle {\sum}_{j=1}^n}\left|{I}_{hkl,j}-\left\langle {I}_{hkl}\right\rangle \right|}{{\displaystyle {\sum}_{hkl}}{\displaystyle {\sum}_j}{I}_{hkl,j}} \)
  5. \( {R}_{\mathrm{p}.\mathrm{i}.\mathrm{m}}=\frac{{\displaystyle {\sum}_{hkl}}\sqrt{\frac{1}{\mathrm{n}-1}}{\displaystyle {\sum}_{j=1}^n}\left|{I}_{hkl,j}-\left\langle {I}_{hkl}\right\rangle \right|}{{\displaystyle {\sum}_{hkl}}{\displaystyle {\sum}_j}{I}_{hkl,j}} \)
  6. where I hkl is the reflection intensity and < I hkl > is the average intensity for multiple measurements of that reflection.