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Structure of human DNA polymerase beta misinserting dAMPNPP opposite the 5'G of the cisplatin Pt-GG intrastrand crosslink
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TUR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295.15 23% PEG 3350, 50 mM Tris (pH 6.5), and 350 mM sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.37 48.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.99 α = 90 b = 79.184 β = 107.6 c = 54.587 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 ADSC QUANTUM 315r 2016-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.9765 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.3 50 100 0.076 0.088 0.045 7.4 3.8 19460
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 2.3 2.34 100 0.346 0.403 0.206 0.89 3.8
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 4TUR 2.3 43.52 17892 968 96.72 0.2036 0.201 0.2059 0.2481 0.2537 RANDOM 38.251
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] 0.01 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.176 r_dihedral_angle_3_deg 16.603 r_dihedral_angle_4_deg 14.286 r_dihedral_angle_1_deg 6.001 r_angle_refined_deg 1.418 r_angle_other_deg 1.361 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.176 r_dihedral_angle_3_deg 16.603 r_dihedral_angle_4_deg 14.286 r_dihedral_angle_1_deg 6.001 r_angle_refined_deg 1.418 r_angle_other_deg 1.361 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2538 Nucleic Acid Atoms 632 Solvent Atoms 69 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement PHENIX refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction REFMAC phasing