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Human DNA polymerase beta 8-oxoG:dA extension with dTTP after 120 s
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 imidazole pH 7.0-7.5, 350 mM sodium acetate, 16-18% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.23 44.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.8 α = 90 b = 79.7 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 MX300HE 2015-11-12 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 1.87 48.55 93.5 0.038 0.052 0.998 13.53 1.917 64194 -3 27.493
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 1.87 1.9 95.4 0.389 0.532 0.846 2.09 1.893
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 1.87 48.55 32063 1688 96.74 0.2017 0.1988 0.2061 0.2569 0.264 RANDOM 26.703
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] 0.19 -0.2 0.4 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.312 r_dihedral_angle_4_deg 16.582 r_dihedral_angle_3_deg 14.419 r_dihedral_angle_1_deg 5.499 r_angle_refined_deg 1.401 r_angle_other_deg 1.07 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.312 r_dihedral_angle_4_deg 16.582 r_dihedral_angle_3_deg 14.419 r_dihedral_angle_1_deg 5.499 r_angle_refined_deg 1.401 r_angle_other_deg 1.07 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2619 Nucleic Acid Atoms 654 Solvent Atoms 340 Heterogen Atoms 27
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data scaling PHASER phasing XDS data reduction