3BGF

X-ray crystal structure of the SARS coronavirus spike receptor binding domain in complex with F26G19 Fab


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52980.1 M MES, 14% PEG 20000, 10-15% glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthew coefficientSolvent content
2.7154.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 183.688α = 90
b = 73.365β = 90
c = 110.782γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12C0.979NSLSX12C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.85094.40.1326.35.23761435508-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.82.969.90.7512.92587

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entries 2DDB, 1KEG3303076030321149598.730.2370.2340.286RANDOM46.995
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.985
r_dihedral_angle_4_deg14.718
r_dihedral_angle_3_deg12.486
r_dihedral_angle_1_deg3.204
r_mcangle_it1.139
r_angle_refined_deg1.077
r_mcbond_it0.647
r_scangle_it0.548
r_symmetry_hbond_refined0.426
r_scbond_it0.336
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.985
r_dihedral_angle_4_deg14.718
r_dihedral_angle_3_deg12.486
r_dihedral_angle_1_deg3.204
r_mcangle_it1.139
r_angle_refined_deg1.077
r_mcbond_it0.647
r_scangle_it0.548
r_symmetry_hbond_refined0.426
r_scbond_it0.336
r_nbtor_refined0.328
r_nbd_refined0.246
r_xyhbond_nbd_refined0.199
r_symmetry_vdw_refined0.198
r_chiral_restr0.074
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9411
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling