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Structure of the E9 DNA polymerase from vaccinia virus in complex with manganese
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N2E
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, 5 mM MnCl2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.007 α = 90 b = 134.007 β = 90 c = 230.189 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 2015-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0714 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 2.78 46 99.1 0.108 11.6 3.4 59597
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 2.79 2.89 99.2 0.958 1.8 3.5 5772
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5N2E 2.78 46 56628 2911 97.35 0.18548 0.18333 0.22721 0.2129 RANDOM 72.326
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] 1.33 0.67 1.33 -4.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.156 r_dihedral_angle_3_deg 18.989 r_dihedral_angle_4_deg 18.052 r_long_range_B_refined 11.565 r_long_range_B_other 11.564 r_scangle_other 7.712 r_dihedral_angle_1_deg 7.571 r_mcangle_other 7.339 r_mcangle_it 7.338 r_scbond_it 4.767
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.156 r_dihedral_angle_3_deg 18.989 r_dihedral_angle_4_deg 18.052 r_long_range_B_refined 11.565 r_long_range_B_other 11.564 r_scangle_other 7.712 r_dihedral_angle_1_deg 7.571 r_mcangle_other 7.339 r_mcangle_it 7.338 r_scbond_it 4.767 r_scbond_other 4.767 r_mcbond_it 4.591 r_mcbond_other 4.581 r_angle_refined_deg 1.553 r_angle_other_deg 0.983 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 8171 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing