7LG2

Human leukocyte antigen A*0201 in complex with SARS-CoV2 epitope ALWEIQQVV


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H7BPDB entry 3H7B

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529025% PEG3350, 0.1 M Bis-Tris, pH 5.5, 0.2 M magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
2.6553.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.8α = 90
b = 121.8β = 90
c = 63.644γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rSI 111 CRYSTAL2020-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9794APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.443.061000.0980.9939.4518407
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.441000.361.44.8

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 REPLACEMENTTHROUGHOUTPDB entry 3H7B2.443.061780659699.990.19230.19030.2537RANDOM55.296
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]
14.3614.36-28.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.87
r_dihedral_angle_3_deg16.737
r_dihedral_angle_4_deg15.044
r_dihedral_angle_1_deg7.718
r_angle_refined_deg1.321
r_angle_other_deg1.168
r_chiral_restr0.056
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.87
r_dihedral_angle_3_deg16.737
r_dihedral_angle_4_deg15.044
r_dihedral_angle_1_deg7.718
r_angle_refined_deg1.321
r_angle_other_deg1.168
r_chiral_restr0.056
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3116
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing