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Human DNA polymerase beta crosslinked complex, 60 min Ca to Mg exchange
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RQ1
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 2.46 49.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.416 α = 90 b = 81.772 β = 109.08 c = 55.736 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 2019-07-19 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 2.96 45.27 97.4 0.079 0.093 0.05 0.996 11.9 3.5 9589
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 2.96 3.14 97.2 0.411 0.485 0.255 0.874 3.5
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 4RQ1 2.96 45.27 8547 1016 97.09 0.2519 0.2481 0.2472 0.2837 0.2843 RANDOM 71.55
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] -3.14 4.17 -4.96 4.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.195 r_dihedral_angle_3_deg 15.506 r_dihedral_angle_4_deg 10.7 r_dihedral_angle_1_deg 5.136 r_angle_refined_deg 1.097 r_angle_other_deg 1.087 r_chiral_restr 0.036 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.195 r_dihedral_angle_3_deg 15.506 r_dihedral_angle_4_deg 10.7 r_dihedral_angle_1_deg 5.136 r_angle_refined_deg 1.097 r_angle_other_deg 1.087 r_chiral_restr 0.036 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2493 Nucleic Acid Atoms 647 Solvent Atoms 12 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing