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Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R42 PDB ENTRY 1R42
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 100 mM Tris pH 8.2, 24% PEG6000, 150 mM NaCl, 10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, pH 7.5, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.299 α = 90 b = 119.429 β = 91.97 c = 113.237 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 2005-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 ALS 8.2.1
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 2.8 47.4 93.1 0.085 20.5 6.9 41841
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 93.1 0.682 1.83
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 PDB ENTRY 1R42 2.9 47.4 41841 2165 92.4 0.221 0.218 0.275 0.3051 RANDOM 90.77
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] 0.45 7.05 0.04 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.497 r_dihedral_angle_3_deg 20.62 r_dihedral_angle_4_deg 17.319 r_dihedral_angle_1_deg 5.69 r_scangle_it 1.433 r_angle_refined_deg 1.253 r_mcangle_it 1.234 r_scbond_it 0.855 r_mcbond_it 0.678 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.497 r_dihedral_angle_3_deg 20.62 r_dihedral_angle_4_deg 17.319 r_dihedral_angle_1_deg 5.69 r_scangle_it 1.433 r_angle_refined_deg 1.253 r_mcangle_it 1.234 r_scbond_it 0.855 r_mcbond_it 0.678 r_nbtor_refined 0.317 r_symmetry_hbond_refined 0.24 r_nbd_refined 0.234 r_symmetry_vdw_refined 0.22 r_xyhbond_nbd_refined 0.17 r_metal_ion_refined 0.167 r_chiral_restr 0.089 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12546 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 166
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing