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Human DNA polymerase eta inserting dCMPNPP opposite the 3'G of cisplatin crosslinked Gs (Pt-GG1).
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 6 293 MES, MgCl2, PEG 2K-MME, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.14 42.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.21 α = 90 b = 99.21 β = 90 c = 82.15 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 95 CCD MARMOSAIC 225 mm CCD double Si(220) crystal and mirror vertical focusing 2010-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 30 99.7 0.136 0.12 11.33 4.5 30655 30558 21.51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.06 97.4 0.501 0.588 4.62 3.8 2195
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB ENTRY 3MR2 2 30 1.36 30625 30539 2343 99.72 0.196 0.1943 0.183 0.2172 0.2085 keep the same as used in 3MR2 refinement. Original selection is random. 26.8717
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] 2.7876 2.7876 3.5211
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.582 f_angle_d 0.997 f_chiral_restr 0.091 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3352 Nucleic Acid Atoms 373 Solvent Atoms 209 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction SERGUI data collection XDS data reduction XSCALE data scaling PHENIX phasing