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Structure of vaccinia virus D8 protein bound to human Fab vv66
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E9O 4E9O, 4FQQ experimental model PDB 4FQQ 4E9O, 4FQQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 295 20% PEG 3350, 200 mM sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.61 52.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.857 α = 90 b = 61.515 β = 90 c = 444.405 γ = 90
Symmetry Space Group P 21 21 21
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 2014-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.98 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.23 38.76 99.6 0.081 0.035 15.7 6.2 75859
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.23 2.35 97.5 0.846 0.405 1.9 4.9
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 4E9O, 4FQQ 2.3 38.51 66196 3518 99.89 0.22015 0.21817 0.25699 0.2337 RANDOM 52.615
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] -0.85 -0.8 1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.728 r_dihedral_angle_4_deg 18.802 r_dihedral_angle_3_deg 14.574 r_dihedral_angle_1_deg 6.611 r_long_range_B_refined 2.044 r_long_range_B_other 2.026 r_angle_refined_deg 1.233 r_mcangle_it 0.911 r_mcangle_other 0.911 r_angle_other_deg 0.878
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.728 r_dihedral_angle_4_deg 18.802 r_dihedral_angle_3_deg 14.574 r_dihedral_angle_1_deg 6.611 r_long_range_B_refined 2.044 r_long_range_B_other 2.026 r_angle_refined_deg 1.233 r_mcangle_it 0.911 r_mcangle_other 0.911 r_angle_other_deg 0.878 r_scangle_other 0.756 r_mcbond_it 0.515 r_mcbond_other 0.515 r_scbond_it 0.433 r_scbond_other 0.433 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 10028 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALA data scaling PHASER phasing PDB_EXTRACT data extraction HKL data reduction