3C9N

Crystal Structure of a SARS Corona Virus Derived Peptide Bound to the Human Major Histocompatibility Complex Class I molecule HLA-B*1501


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XR9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.52730.2M Magnesium chloride hexahydrate, 0.1M HEPES sodium, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.5351.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.658α = 90
b = 81.713β = 90
c = 109.391γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray173CCDMAR CCD 165 mm2006-12-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-5MAX III911-5

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
11.8718.2999.80.06415.7438220110.47
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)
1.871.971000.3623.14.1

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 REPLACEMENTTHROUGHOUT1XR91.8718.293830536303191099.80.190.1880.227RANDOM25.82
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]
-0.7-0.691.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.889
r_dihedral_angle_4_deg17.821
r_dihedral_angle_3_deg14.563
r_dihedral_angle_1_deg6.424
r_scangle_it4.09
r_scbond_it2.582
r_mcangle_it1.748
r_angle_refined_deg1.501
r_mcbond_it1.179
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.889
r_dihedral_angle_4_deg17.821
r_dihedral_angle_3_deg14.563
r_dihedral_angle_1_deg6.424
r_scangle_it4.09
r_scbond_it2.582
r_mcangle_it1.748
r_angle_refined_deg1.501
r_mcbond_it1.179
r_nbtor_refined0.304
r_symmetry_hbond_refined0.216
r_nbd_refined0.208
r_symmetry_vdw_refined0.205
r_xyhbond_nbd_refined0.184
r_chiral_restr0.108
r_bond_refined_d0.015
r_gen_planes_refined0.007
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_refined
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 AtomsNumber
Protein Atoms3184
Nucleic Acid Atoms
Solvent Atoms357
Heterogen Atoms28

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction