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Human DNA polymerase beta crosslinked complex, 20 s Ca to Mg exchange
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RPY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 0.1 M Citrate pH 5.5, 18% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.12 41.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.019 α = 90 b = 79.297 β = 105.86 c = 55.125 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 PIXEL DECTRIS PILATUS3 S 6M 2019-07-17 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) Rpim 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 1.93 47.15 96.3 0.034 0.04 0.021 0.999 14.7 3.5 29463
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.97 95.7 0.34 0.406 0.218 0.854 3.3
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 4RPY 1.93 44.12 27983 1472 96.11 0.1875 0.1857 0.1929 0.2204 0.2292 RANDOM 30.486
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] 1.67 -0.15 -0.46 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.805 r_dihedral_angle_4_deg 15.43 r_dihedral_angle_3_deg 14.411 r_dihedral_angle_1_deg 6.102 r_angle_refined_deg 1.579 r_angle_other_deg 1.383 r_chiral_restr 0.1 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.805 r_dihedral_angle_4_deg 15.43 r_dihedral_angle_3_deg 14.411 r_dihedral_angle_1_deg 6.102 r_angle_refined_deg 1.579 r_angle_other_deg 1.383 r_chiral_restr 0.1 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2514 Nucleic Acid Atoms 650 Solvent Atoms 158 Heterogen Atoms 96
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing