6Q3K

Engineered Human HLA_A2 MHC Class I molecule in complex with NV9 peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MRE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2935 mM cobalt chloride, 5 mM cadmium chloride, 5 mM magnesium chloride, 5 mM nickel chloride, 0.1 M HEPES pH 7.5, 12 % PEG 3350.
Crystal Properties
Matthews coefficientSolvent content
2.9758.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.158α = 90
b = 80.575β = 90
c = 109.693γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2017-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9763PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
11.56599.90.0557.35.481571
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.53

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 REPLACEMENTTHROUGHOUT3MRE1.564.9481571426599.850.175520.174280.19955RANDOM23.012
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]
-0.730.650.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.961
r_dihedral_angle_4_deg20.309
r_dihedral_angle_3_deg13.235
r_dihedral_angle_1_deg11.111
r_long_range_B_refined8.581
r_long_range_B_other8.363
r_scangle_other6.574
r_scbond_it4.549
r_scbond_other4.541
r_mcangle_it3.919
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.961
r_dihedral_angle_4_deg20.309
r_dihedral_angle_3_deg13.235
r_dihedral_angle_1_deg11.111
r_long_range_B_refined8.581
r_long_range_B_other8.363
r_scangle_other6.574
r_scbond_it4.549
r_scbond_other4.541
r_mcangle_it3.919
r_mcangle_other3.918
r_mcbond_other2.875
r_mcbond_it2.874
r_angle_refined_deg1.508
r_angle_other_deg0.782
r_chiral_restr0.123
r_gen_planes_refined0.015
r_bond_refined_d0.013
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3142
Nucleic Acid Atoms
Solvent Atoms589
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing