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Crystal Structure of Human DNA Polymerase Eta Inserting dAMPNPP Opposite O4-Ethylthymidine
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, 22% PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.11 41.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.82 α = 90 b = 98.82 β = 90 c = 82.017 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 2014-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.29 59.21 100 0.155 0.155 8.4 5.6 20600 20600 -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 2.29 2.35 100 0.595 3.2 5.6
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 2.29 59.21 19497 1071 99.99 0.17836 0.17579 0.1789 0.22678 0.2302 RANDOM 31.071
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] -0.45 -0.22 -0.45 1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.654 r_dihedral_angle_4_deg 17.623 r_dihedral_angle_3_deg 15.014 r_long_range_B_other 7.231 r_long_range_B_refined 7.23 r_dihedral_angle_1_deg 5.927 r_scangle_other 4.407 r_mcangle_it 3.362 r_mcangle_other 3.361 r_scbond_it 2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.654 r_dihedral_angle_4_deg 17.623 r_dihedral_angle_3_deg 15.014 r_long_range_B_other 7.231 r_long_range_B_refined 7.23 r_dihedral_angle_1_deg 5.927 r_scangle_other 4.407 r_mcangle_it 3.362 r_mcangle_other 3.361 r_scbond_it 2.86 r_scbond_other 2.86 r_mcbond_it 2.169 r_mcbond_other 2.161 r_angle_refined_deg 1.422 r_angle_other_deg 1.09 r_chiral_restr 0.073 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 389 Solvent Atoms 212 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing