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X-ray crystal structure of the SARS coronavirus spike receptor binding domain in complex with F26G19 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DDB PDB entries 2DDB, 1KEG experimental model PDB 1KEG PDB entries 2DDB, 1KEG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 0.1 M MES, 14% PEG 20000, 10-15% glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.71 54.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.688 α = 90 b = 73.365 β = 90 c = 110.782 γ = 90
Symmetry Space Group P 21 21 2
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 MAR CCD 165 mm 2006-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 0.979 NSLS X12C
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 2.8 50 94.4 0.132 6.3 5.2 37614 35508 -3
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) 2.8 2.9 69.9 0.751 2.9 2587
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 (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 2DDB, 1KEG 3 30 30760 30321 1495 98.73 0.237 0.234 0.2422 0.286 0.2923 RANDOM 46.995
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] 7.4 -0.5 -6.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.985 r_dihedral_angle_4_deg 14.718 r_dihedral_angle_3_deg 12.486 r_dihedral_angle_1_deg 3.204 r_mcangle_it 1.139 r_angle_refined_deg 1.077 r_mcbond_it 0.647 r_scangle_it 0.548 r_symmetry_hbond_refined 0.426 r_scbond_it 0.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.985 r_dihedral_angle_4_deg 14.718 r_dihedral_angle_3_deg 12.486 r_dihedral_angle_1_deg 3.204 r_mcangle_it 1.139 r_angle_refined_deg 1.077 r_mcbond_it 0.647 r_scangle_it 0.548 r_symmetry_hbond_refined 0.426 r_scbond_it 0.336 r_nbtor_refined 0.328 r_nbd_refined 0.246 r_xyhbond_nbd_refined 0.199 r_symmetry_vdw_refined 0.198 r_chiral_restr 0.074 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9411 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction HKL-2000 data scaling