7Q99

MHC Class I A02 Allele presenting NLSALGIFST, 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 HEPES, 25% PEG 4000, 15% Glycerol, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
3.1861.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.28α = 90
b = 121.28β = 90
c = 81.314γ = 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
12.5560.651000.1970.2110.0750.9957.27.87073153.5
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)
12.552.591003.864.151.520.2210.47.4

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 REPLACEMENTTHROUGHOUT3HG12.5560.6436363190599.010.22090.21830.2722RANDOM72.408
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]
-1.07-1.072.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.177
r_dihedral_angle_4_deg18.952
r_dihedral_angle_3_deg17.616
r_dihedral_angle_1_deg9.241
r_angle_refined_deg1.454
r_angle_other_deg1.168
r_chiral_restr0.057
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.177
r_dihedral_angle_4_deg18.952
r_dihedral_angle_3_deg17.616
r_dihedral_angle_1_deg9.241
r_angle_refined_deg1.454
r_angle_other_deg1.168
r_chiral_restr0.057
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6619
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms8

Software

Software
Software NamePurpose
XDSdata reduction
xia2data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction