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Structure of the E9 DNA polymerase from vaccinia virus
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 = 133.415 α = 90 b = 133.415 β = 90 c = 230.525 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 2014-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976 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 2.74 46 99.9 0.077 18.2 5.3 63014
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 2.74 2.81 99.9 0.728 2.8 5.1 4369
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MIR THROUGHOUT 2.74 115.81 59888 3075 99.79 0.18849 0.18605 0.1906 0.23561 0.2365 RANDOM 73.966
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] 0.15 0.07 0.15 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.097 r_dihedral_angle_3_deg 19.768 r_dihedral_angle_4_deg 18.225 r_long_range_B_other 13.568 r_long_range_B_refined 13.567 r_scangle_other 9.934 r_mcangle_it 9.167 r_mcangle_other 9.166 r_dihedral_angle_1_deg 7.666 r_scbond_it 6.656
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.097 r_dihedral_angle_3_deg 19.768 r_dihedral_angle_4_deg 18.225 r_long_range_B_other 13.568 r_long_range_B_refined 13.567 r_scangle_other 9.934 r_mcangle_it 9.167 r_mcangle_other 9.166 r_dihedral_angle_1_deg 7.666 r_scbond_it 6.656 r_scbond_other 6.655 r_mcbond_it 6.185 r_mcbond_other 6.183 r_angle_refined_deg 1.855 r_angle_other_deg 1.076 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.003 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 8171 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling SOLVE phasing