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Crystal structure of human DNA polymerase eta in ternary complex with a cisplatin DNA adduct
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MR2 PDB ENTRY 3MR2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 15-35% PEG1500, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.09 41.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.5 α = 90 b = 98.5 β = 90 c = 82.603 γ = 120
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 PILATUS 6M 2011-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.0722 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.32 50 99.85 0.108 16.9 6.2 19767 19734 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.32 2.38 99.9 0.462 3.8 5.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 3MR2 2.32 49.25 19764 18206 1528 99.85 0.18247 0.18247 0.17834 0.1833 0.23253 0.2315 RANDOM 34.458
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] -0.4 -0.2 -0.4 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.332 r_dihedral_angle_4_deg 17.095 r_dihedral_angle_3_deg 14.103 r_dihedral_angle_1_deg 5.028 r_scangle_it 1.618 r_angle_refined_deg 1.134 r_scbond_it 1.079 r_mcangle_it 0.605 r_mcbond_it 0.299 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.332 r_dihedral_angle_4_deg 17.095 r_dihedral_angle_3_deg 14.103 r_dihedral_angle_1_deg 5.028 r_scangle_it 1.618 r_angle_refined_deg 1.134 r_scbond_it 1.079 r_mcangle_it 0.605 r_mcbond_it 0.299 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3255 Nucleic Acid Atoms 388 Solvent Atoms 116 Heterogen Atoms 32
Software Software Software Name Purpose CBASS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling