7Q9A

MHC Class I A02 Allele presenting LLLGIGILVL, in complex with Mel5 TCR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HG1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52930.1M TRIS, 15% PEG 8000, 15% Glycerol, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
3.2662.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.019α = 90
b = 122.019β = 90
c = 82.418γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2020-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97951DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.161.021000.1050.1130.040.99810.67.77073144
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.141002.62.80.9890.3127.8

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 REPLACEMENTTHROUGHOUT3HG12.161.0167098345499.780.20640.20450.2432RANDOM63.387
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]
-1-11.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.952
r_dihedral_angle_4_deg19.777
r_dihedral_angle_3_deg17.391
r_dihedral_angle_1_deg8.602
r_angle_refined_deg1.676
r_angle_other_deg1.264
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.952
r_dihedral_angle_4_deg19.777
r_dihedral_angle_3_deg17.391
r_dihedral_angle_1_deg8.602
r_angle_refined_deg1.676
r_angle_other_deg1.264
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6629
Nucleic Acid Atoms
Solvent Atoms228
Heterogen Atoms24

Software

Software
Software NamePurpose
XDSdata reduction
xia2data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction