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Crystal Structure of Human DNA Polymerase Eta Inserting dTMPNPP Opposite O6-Methyl-2'-deoxyguanosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4O3N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 0.1 M MES pH 5.5, 5mM Magnesium chloride, 16% PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.11 41.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.004 α = 90 b = 99.004 β = 90 c = 81.704 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 CCD MARMOSAIC 300 mm CCD 2013-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.07810 APS 21-ID-D
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 1.94 50 100 0.091 0.091 27.375 7.6 33771 -3
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 1.94 1.97 100 0.819 2.548 7.5
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 4O3N 1.94 50 32023 1715 99.98 0.1608 0.15857 0.1657 0.20166 0.2099 RANDOM 33.677
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] -0.16 -0.08 -0.16 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.435 r_dihedral_angle_4_deg 15.404 r_dihedral_angle_3_deg 14.963 r_long_range_B_refined 8.152 r_long_range_B_other 8.017 r_dihedral_angle_1_deg 6.275 r_scangle_other 5.541 r_mcangle_it 4.228 r_mcangle_other 4.227 r_scbond_it 3.769
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.435 r_dihedral_angle_4_deg 15.404 r_dihedral_angle_3_deg 14.963 r_long_range_B_refined 8.152 r_long_range_B_other 8.017 r_dihedral_angle_1_deg 6.275 r_scangle_other 5.541 r_mcangle_it 4.228 r_mcangle_other 4.227 r_scbond_it 3.769 r_scbond_other 3.768 r_mcbond_other 3.013 r_mcbond_it 3.012 r_angle_refined_deg 1.886 r_angle_other_deg 1.132 r_chiral_restr 0.115 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3366 Nucleic Acid Atoms 390 Solvent Atoms 410 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing