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Crystal Structure of SARS-CoV Spike Receptor-Binding Domain Complexed with Neutralizing Antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AJF PDB ENTRIES 2AJF, 1AZ6 experimental model PDB 1AZ6 PDB ENTRIES 2AJF, 1AZ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 15v/v% Glycerol, 20% PEG 6000, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 49.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.693 α = 90 b = 68.611 β = 98.08 c = 80.085 γ = 90
Symmetry Space Group P 1 21 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 CCD BRUKER PROTEUM 300 mirror 2005-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 30 91 0.06 24.8 3 28540 28540 42.9
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 2.3 2.38 72.8 0.263 2.2 2 2244
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRIES 2AJF, 1AZ6 2.3 29.02 27719 27719 1339 89.3 0.202 0.199 0.199 0.1992 0.261 0.2611 RANDOM 49.7
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] -5.01 6.88 -6.41 11.42
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.8 c_scangle_it 7.39 c_scbond_it 5.84 c_mcangle_it 5.28 c_mcbond_it 3.71 c_angle_deg 1.3 c_improper_angle_d 0.83 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.8 c_scangle_it 7.39 c_scbond_it 5.84 c_mcangle_it 5.28 c_mcbond_it 3.71 c_angle_deg 1.3 c_improper_angle_d 0.83 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4740 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 19
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling PHASER phasing