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

Schormann, Norbert; Banerjee, Surajit; Ricciardi, Robert; Chattopadhyay, Debasish

doi:10.1186/s12900-015-0037-1

BMC Structural Biology

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
R_merge ^b,c	0.158 (0.505)
R_meas ^b,c	0.190 (0.609)
R_pim ^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)
CC_1/2	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)
R_cryst (%)^d	21.6 (29.7)
R_free (%)^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)	0.82^e,f
Ramachandran allowed (%)	99.5
Ramachandran disallowed (%)	0.5 [2 outliers, 1 in each subunit]
MolProbity clash score	8.7 [97^th percentile]
MolProbity score	1.9 [99^th percentile]

^aValues in parentheses represent highest resolution shell
^bR_measand R_pimwere calculated with SCALA [38] in the CCP4 program suite [39] using unmerged and not scaled data preprocessed by XDS [36, 37]. R_measis a merging R-factor independent of data redundancy while R_pim provides the precision of the averaged measurement, which improves with higher multiplicity [48] \( \begin{array}{l}{\mathsf{R}}_{\mathsf{m}\mathrm{e}\mathsf{r}\mathsf{g}\mathrm{e}}={\displaystyle \sum_{\mathsf{hkl}}{\displaystyle \sum_{\mathsf{i}}\Big|{\mathsf{l}}_{\mathsf{i}}\left(\mathsf{h}\mathsf{k}\mathsf{l}\right)-<\mathsf{l}\left(\mathsf{h}\mathsf{k}\mathsf{l}\right)>\mathsf{l}/}}{\displaystyle \sum_{\mathsf{hkl}}{\displaystyle \sum_{\mathsf{i}}{\mathsf{l}}_{\mathsf{i}}\left(\mathsf{h}\mathsf{k}\mathsf{l}\right)}}\hfill \\ {}{\mathsf{R}}_{\mathsf{m}\mathrm{e}\mathsf{a}\mathsf{s}}={\displaystyle \sum_{\mathsf{hkl}}\sqrt{\mathit{\mathsf{N}}/\left(\mathit{\mathsf{N}}-\mathsf{1}\right)}{\displaystyle \sum_{\mathsf{i}}\Big|{\mathsf{l}}_{\mathsf{i}}\left(\mathsf{h}\mathsf{k}\mathsf{l}\right)-<\mathsf{l}\left(\mathsf{h}\mathsf{k}\mathsf{l}\right)>\mathsf{l}/}{\displaystyle \sum_{\mathsf{hkl}}{\displaystyle \sum_{\mathsf{i}}{\mathsf{l}}_{\mathsf{i}}\left(\mathsf{h}\mathsf{k}\mathsf{l}\right)}}}\hfill \\ {}{\mathsf{R}}_{\mathsf{pim}}={\displaystyle \sum_{\mathsf{hkl}}\sqrt{\mathsf{1}/\left(\mathit{\mathsf{N}}-\mathsf{1}\right)}{\displaystyle \sum_{\mathsf{i}}\Big|{\mathsf{l}}_{\mathsf{i}}\left(\mathsf{h}\mathsf{k}\mathsf{l}\right)-<\mathsf{l}\left(\mathsf{h}\mathsf{k}\mathsf{l}\right)>\mathsf{l}/}{\displaystyle \sum_{\mathsf{hkl}}{\displaystyle \sum_{\mathsf{i}}{\mathsf{l}}_{\mathsf{i}}\left(\mathsf{h}\mathsf{k}\mathsf{l}\right)}}}\hfill \end{array} \)
^cR values for the low resolution shell of 56.50-9.14 Å are: R_merge 0.053; R_meas 0.065; R_pim 0.037
^dThe data included in the R_free set (5 %) were excluded from refinement
^eFinal R and R_free values based on map calculation in PHENIX [45, 46] are 20.8 % and 24.7 %, respectively
^fFinal R and R_free values based on comprehensive validation in PHENIX [45, 46] are 21.5 % and 26.8 %, respectively

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