X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UTQPDB entry 3UTQ for the MHC part and 4UTQ for the TCR part.
experimental modelPDB 4UTQPDB entry 3UTQ for the MHC part and 4UTQ for the TCR part.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2910.1M HEPES, pH 7.5, 15% PEG 4000, 0.2M sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.7555.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.94α = 96.98
b = 100.28β = 98.05
c = 122.44γ = 96.53
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97630DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)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
12.0342.7697.60.050.0690.04682128366128366
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.032.0896.70.2680.2680.4282.81.99447

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 3UTQ for the MHC part and 4UTQ for the TCR part.2.0342.76121919644697.550.1940.19210.2307RANDOM52.559
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]
1.910.29-0.770.950.6-2.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.023
r_dihedral_angle_4_deg20.99
r_dihedral_angle_3_deg19.315
r_dihedral_angle_1_deg7.527
r_mcangle_it2.306
r_angle_refined_deg1.923
r_mcbond_other1.504
r_mcbond_it1.503
r_angle_other_deg1.269
r_chiral_restr0.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.023
r_dihedral_angle_4_deg20.99
r_dihedral_angle_3_deg19.315
r_dihedral_angle_1_deg7.527
r_mcangle_it2.306
r_angle_refined_deg1.923
r_mcbond_other1.504
r_mcbond_it1.503
r_angle_other_deg1.269
r_chiral_restr0.144
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.005
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13402
Nucleic Acid Atoms
Solvent Atoms472
Heterogen Atoms306

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction