☰ Navigation Tabs
Crystal structure of SARS spike protein receptor binding domain in complex with a neutralizing antibody, 80R
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AJF 2AJF CHAIN F, 1DZB CHAIN A experimental model PDB 1DZB 2AJF CHAIN F, 1DZB CHAIN A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 290 12.5% PEG4000, 0.1M sodium acetate, 0.2M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.87 57.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.453 α = 90 b = 175.902 β = 96.55 c = 67.561 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 ADSC QUANTUM 4 2005-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.11587 ALS 5.0.3
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 2.29 50 93.8 0.145 8.8 3.1 51915 51915 -4
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) 2.29 2.38 87 0.571 1.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2AJF CHAIN F, 1DZB CHAIN A 2.3 45.55 43380 2308 93.83 0.25085 0.24843 0.2633 0.29537 0.2704 RANDOM 17.106
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] -1.64 0.51 -2.58 4.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.323 r_dihedral_angle_3_deg 14.71 r_dihedral_angle_4_deg 13.268 r_dihedral_angle_1_deg 6.662 r_scangle_it 1.308 r_angle_refined_deg 1.217 r_scbond_it 0.877 r_angle_other_deg 0.85 r_mcangle_it 0.612 r_mcbond_it 0.524
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.323 r_dihedral_angle_3_deg 14.71 r_dihedral_angle_4_deg 13.268 r_dihedral_angle_1_deg 6.662 r_scangle_it 1.308 r_angle_refined_deg 1.217 r_scbond_it 0.877 r_angle_other_deg 0.85 r_mcangle_it 0.612 r_mcbond_it 0.524 r_symmetry_vdw_other 0.191 r_nbd_other 0.19 r_nbtor_refined 0.18 r_symmetry_vdw_refined 0.177 r_xyhbond_nbd_refined 0.171 r_nbd_refined 0.165 r_symmetry_hbond_refined 0.145 r_nbtor_other 0.079 r_chiral_restr 0.073 r_mcbond_other 0.069 r_xyhbond_nbd_other 0.053 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6614 Nucleic Acid Atoms Solvent Atoms 470 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing PHASER phasing