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vaccinia virus D4/A20(1-50) in complex with dsDNA containing an abasic site and free uracyl
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OD8 4OD8,1SSP experimental model PDB 1SSP 4OD8,1SSP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 293 0.2M ammonium chloride, 10% W/V PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.73 67.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.092 α = 90 b = 136.092 β = 90 c = 161.073 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 PIXEL DECTRIS PILATUS 6M 2014-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9763 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 48.86 99.9 0.045 19.1 5 46345
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 2.7 2.79 100 0.492 2.9 5.2
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 4OD8,1SSP 2.7 48.86 44109 2227 99.87 0.18227 0.17993 0.1867 0.22764 0.2313 RANDOM 73.761
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] 0.29 0.14 0.29 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.468 r_dihedral_angle_3_deg 18.443 r_dihedral_angle_4_deg 17.286 r_long_range_B_refined 12.004 r_long_range_B_other 12.004 r_scangle_other 9.702 r_mcangle_it 8.302 r_mcangle_other 8.301 r_dihedral_angle_1_deg 7.456 r_scbond_it 6.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.468 r_dihedral_angle_3_deg 18.443 r_dihedral_angle_4_deg 17.286 r_long_range_B_refined 12.004 r_long_range_B_other 12.004 r_scangle_other 9.702 r_mcangle_it 8.302 r_mcangle_other 8.301 r_dihedral_angle_1_deg 7.456 r_scbond_it 6.81 r_scbond_other 6.809 r_mcbond_it 5.943 r_mcbond_other 5.943 r_angle_refined_deg 1.82 r_angle_other_deg 1.348 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.006 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 6558 Nucleic Acid Atoms 1188 Solvent Atoms 54 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing