7NME

Human MHC Class I, A24 Allele presenting QLPRLFPLL, Complex with 4C6 TCR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BCK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9291Molecular Dimensions Pact Premier C06: 0.1M PCTCP buffer, 25% PEG 1500, pH 9.0
Crystal Properties
Matthews coefficientSolvent content
2.2946.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.163α = 90
b = 71.347β = 90
c = 220.185γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97623DiamondI03

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
12.2110.0999.50.1790.20.0870.9895.95.144950
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)
12.22.2795.11.551.7310.7620.3555.2

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 REPLACEMENTTHROUGHOUT2BCK2.2110.0942709216999.540.21770.21490.2737RANDOM38.126
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]
-1.590.850.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.646
r_dihedral_angle_4_deg17.815
r_dihedral_angle_3_deg17.362
r_dihedral_angle_1_deg8.828
r_angle_refined_deg1.168
r_angle_other_deg1.094
r_chiral_restr0.044
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.646
r_dihedral_angle_4_deg17.815
r_dihedral_angle_3_deg17.362
r_dihedral_angle_1_deg8.828
r_angle_refined_deg1.168
r_angle_other_deg1.094
r_chiral_restr0.044
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6591
Nucleic Acid Atoms
Solvent Atoms200
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
xia2data reduction
XDSdata reduction