2GHW

Crystal structure of SARS spike protein receptor binding domain in complex with a neutralizing antibody, 80R


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AJF2AJF CHAIN F, 1DZB CHAIN A
experimental modelPDB 1DZB2AJF CHAIN F, 1DZB CHAIN A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.629012.5% PEG4000, 0.1M sodium acetate, 0.2M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.8757.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.453α = 90
b = 175.902β = 96.55
c = 67.561γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-09-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.31.11587ALS5.0.3

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
12.295093.80.1458.83.15191551915-4
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)
2.292.38870.5711.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2AJF CHAIN F, 1DZB CHAIN A2.345.5543380230893.830.250850.248430.29537RANDOM17.106
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]
-1.640.51-2.584.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.323
r_dihedral_angle_3_deg14.71
r_dihedral_angle_4_deg13.268
r_dihedral_angle_1_deg6.662
r_scangle_it1.308
r_angle_refined_deg1.217
r_scbond_it0.877
r_angle_other_deg0.85
r_mcangle_it0.612
r_mcbond_it0.524
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.323
r_dihedral_angle_3_deg14.71
r_dihedral_angle_4_deg13.268
r_dihedral_angle_1_deg6.662
r_scangle_it1.308
r_angle_refined_deg1.217
r_scbond_it0.877
r_angle_other_deg0.85
r_mcangle_it0.612
r_mcbond_it0.524
r_symmetry_vdw_other0.191
r_nbd_other0.19
r_nbtor_refined0.18
r_symmetry_vdw_refined0.177
r_xyhbond_nbd_refined0.171
r_nbd_refined0.165
r_symmetry_hbond_refined0.145
r_nbtor_other0.079
r_chiral_restr0.073
r_mcbond_other0.069
r_xyhbond_nbd_other0.053
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms6614
Nucleic Acid Atoms
Solvent Atoms470
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHASERphasing