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Human DNA polymerase beta pre-catalytic 8-oxoG:dC extension complex with dTTP bound in non-planar conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RPX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 50 mM imidizole pH 7-7.5, 350 mM sodium acetate, 16-18 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.23 44.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.7 α = 90 b = 79.5 β = 107.1 c = 55.3 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX225HE 2016-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.58 52.85 98 0.066 0.091 0.994 11.46 1.975 25529 -3 42.01
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.58 2.6 100 0.406 0.557 0.666 2.02 1.965
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4RPX 2.58 52.85 12586 663 99.5 0.2377 0.2342 0.2369 0.306 0.303 RANDOM 35.854
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.03 0.1 -0.13 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.114 r_dihedral_angle_3_deg 11.604 r_dihedral_angle_4_deg 10.949 r_dihedral_angle_1_deg 4.406 r_angle_refined_deg 0.893 r_angle_other_deg 0.783 r_chiral_restr 0.047 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.114 r_dihedral_angle_3_deg 11.604 r_dihedral_angle_4_deg 10.949 r_dihedral_angle_1_deg 4.406 r_angle_refined_deg 0.893 r_angle_other_deg 0.783 r_chiral_restr 0.047 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2573 Nucleic Acid Atoms 632 Solvent Atoms 48 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data scaling PHASER phasing SCALEPACK data scaling