Skip to main content

Advertisement

Table 2 Data collection and refinement statistics for 4qcb

From: Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA Glycosylase

Wavelength [Å] 0.97918
Space group P212121
Unit cell parameters [Å] a = 39.40, b = 92.32, c = 142.88
Data collection statistics  
Resolution limit [Å] 56.50-2.89 (3.05-2.89)a
Rmerge b,c 0.158 (0.505)
Rmeas b,c 0.190 (0.609)
Rpim b,c 0.105 (0.335)
Total number of observations 35850 (5327)
Total number unique 11991 (1750)
Mean I/σ (I) 6.1 (2.3)
CC1/2 0.986 (0.855)
CC* 0.996 (0.960)
Completeness [%] 97.9 (99.3)
Multiplicity 3.0 (3.0)
Refinement statistics  
Resolution range (Å) 56.50 - 2.89 (2.97 - 2.89)a
Number of unique reflections 11966 (886)
Completeness (%) 97.3 (99.1)
Rcryst (%)d 21.6 (29.7)
Rfree (%)d 26.5 (32.6)
No. of protein residues 426
No. of DNA nucleotides 22
No. of GOL molecules 4
No. of water molecules 118
Wilson B-factor (Å2) 29.4
Average B-factors (Å2)  
Overall 31.4
Protein 28.5
DNA 56.5
GOL 36.6
Water 18.6
Coordinate error (maximum likelihood) 0.39
Correlation coefficient Fo-Fc 0.93
Correlation coefficient Fo-Fc free 0.88
Overall map CC (Fc, 2mFo-DFc) 0.82e,f
Ramachandran allowed (%) 99.5
Ramachandran disallowed (%) 0.5 [2 outliers, 1 in each subunit]
MolProbity clash score 8.7 [97th percentile]
MolProbity score 1.9 [99th percentile]
  1. aValues in parentheses represent highest resolution shell
  2. bRmeasand Rpimwere calculated with SCALA [38] in the CCP4 program suite [39] using unmerged and not scaled data preprocessed by XDS [36, 37]. Rmeasis a merging R-factor independent of data redundancy while Rpim provides the precision of the averaged measurement, which improves with higher multiplicity [48] \( \begin{array}{l}{\mathsf{R}}_{\mathsf{m}\mathrm{e}\mathsf{r}\mathsf{g}\mathrm{e}}={\displaystyle \sum_{\mathsf{hkl}}{\displaystyle \sum_{\mathsf{i}}\Big|{\mathsf{l}}_{\mathsf{i}}\left(\mathsf{h}\mathsf{k}\mathsf{l}\right)-<\mathsf{l}\left(\mathsf{h}\mathsf{k}\mathsf{l}\right)>\mathsf{l}/}}{\displaystyle \sum_{\mathsf{hkl}}{\displaystyle \sum_{\mathsf{i}}{\mathsf{l}}_{\mathsf{i}}\left(\mathsf{h}\mathsf{k}\mathsf{l}\right)}}\hfill \\ {}{\mathsf{R}}_{\mathsf{m}\mathrm{e}\mathsf{a}\mathsf{s}}={\displaystyle \sum_{\mathsf{hkl}}\sqrt{\mathit{\mathsf{N}}/\left(\mathit{\mathsf{N}}-\mathsf{1}\right)}{\displaystyle \sum_{\mathsf{i}}\Big|{\mathsf{l}}_{\mathsf{i}}\left(\mathsf{h}\mathsf{k}\mathsf{l}\right)-<\mathsf{l}\left(\mathsf{h}\mathsf{k}\mathsf{l}\right)>\mathsf{l}/}{\displaystyle \sum_{\mathsf{hkl}}{\displaystyle \sum_{\mathsf{i}}{\mathsf{l}}_{\mathsf{i}}\left(\mathsf{h}\mathsf{k}\mathsf{l}\right)}}}\hfill \\ {}{\mathsf{R}}_{\mathsf{pim}}={\displaystyle \sum_{\mathsf{hkl}}\sqrt{\mathsf{1}/\left(\mathit{\mathsf{N}}-\mathsf{1}\right)}{\displaystyle \sum_{\mathsf{i}}\Big|{\mathsf{l}}_{\mathsf{i}}\left(\mathsf{h}\mathsf{k}\mathsf{l}\right)-<\mathsf{l}\left(\mathsf{h}\mathsf{k}\mathsf{l}\right)>\mathsf{l}/}{\displaystyle \sum_{\mathsf{hkl}}{\displaystyle \sum_{\mathsf{i}}{\mathsf{l}}_{\mathsf{i}}\left(\mathsf{h}\mathsf{k}\mathsf{l}\right)}}}\hfill \end{array} \)
  3. cR values for the low resolution shell of 56.50-9.14 Å are: Rmerge 0.053; Rmeas 0.065; Rpim 0.037
  4. dThe data included in the Rfree set (5 %) were excluded from refinement
  5. eFinal R and Rfree values based on map calculation in PHENIX [45, 46] are 20.8 % and 24.7 %, respectively
  6. fFinal R and Rfree values based on comprehensive validation in PHENIX [45, 46] are 21.5 % and 26.8 %, respectively