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Structure of the E9 DNA polymerase exonuclease deficient mutant (D166A+E168A) from vaccinia virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N2G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.25 293 9-11% PEG 3000, 20-25% glycerol, 100 mM MES-NaOH pH 6.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.524 α = 90 b = 133.524 β = 90 c = 229.492 γ = 120
Symmetry Space Group P 31 2 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 PIXEL DECTRIS PILATUS 6M-F 2015-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.2724 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.81 57 99 0.089 11.3 3.3 57789
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.81 2.96 97.1 0.788 1.8 3.2 8176
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 5N2G 2.81 57 54943 2805 97.61 0.18662 0.18481 0.1894 0.22165 0.2229 RANDOM 77.725
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] 1.4 0.7 1.4 -4.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.957 r_dihedral_angle_4_deg 19.269 r_dihedral_angle_3_deg 19.211 r_long_range_B_other 12.58 r_long_range_B_refined 12.579 r_scangle_other 8.817 r_mcangle_it 7.83 r_mcangle_other 7.829 r_dihedral_angle_1_deg 7.801 r_scbond_it 5.536
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.957 r_dihedral_angle_4_deg 19.269 r_dihedral_angle_3_deg 19.211 r_long_range_B_other 12.58 r_long_range_B_refined 12.579 r_scangle_other 8.817 r_mcangle_it 7.83 r_mcangle_other 7.829 r_dihedral_angle_1_deg 7.801 r_scbond_it 5.536 r_scbond_other 5.534 r_mcbond_it 4.982 r_mcbond_other 4.98 r_angle_refined_deg 1.617 r_angle_other_deg 0.998 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 8164 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing