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Structure of vaccinia virus D8 protein bound to human Fab vv304
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E9O 4E9O, 3LMJ experimental model PDB 3LMJ 4E9O, 3LMJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 20% PEG 4000, 200 mM sodium citrate tribasic
Crystal Properties Matthews coefficient Solvent content 2.48 50.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.98 α = 90 b = 117.98 β = 90 c = 104.6 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2014-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.15 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.9 47.81 94.8 0.0112 6.5 3.2 30196
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.06 97.1 0.57 1.5 3.3
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 4E9O, 3LMJ 2.9 47.81 28658 1537 94.65 0.2493 0.2468 0.2459 0.2973 0.2929 RANDOM 56.55
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] -0.01 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.822 r_dihedral_angle_3_deg 12.986 r_dihedral_angle_4_deg 11.222 r_dihedral_angle_1_deg 5.286 r_angle_refined_deg 0.847 r_angle_other_deg 0.648 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.822 r_dihedral_angle_3_deg 12.986 r_dihedral_angle_4_deg 11.222 r_dihedral_angle_1_deg 5.286 r_angle_refined_deg 0.847 r_angle_other_deg 0.648 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10022 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection DENZO data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL data reduction