2PYF

Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC RevealNative Diagonal Binding Geometry Unbound TCR Clone 5-1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529185 mM Na HEPES buffer pH7.5, 8.5 % iso-propanol, 17% PEG 4000, 15% glycerol, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1242.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.964α = 90
b = 59.805β = 90.94
c = 81.799γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MIRROR + MONOCHROMATOR2005-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.1SRSPX14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
12.230970.1390.1393.93.220741
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.3290.80.6710.0791.33.1701

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 REPLACEMENTTHROUGHOUT2BNR2.2301953210640.213480.209190.29484RANDOM17.403
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]
-0.971.45-0.461.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg16.478
r_scangle_it7.772
r_dihedral_angle_3_deg5.8
r_scbond_it5.795
r_dihedral_angle_4_deg4.772
r_mcangle_it4.102
r_mcbond_it2.771
r_dihedral_angle_1_deg1.269
r_angle_refined_deg1.253
r_angle_other_deg0.722
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg16.478
r_scangle_it7.772
r_dihedral_angle_3_deg5.8
r_scbond_it5.795
r_dihedral_angle_4_deg4.772
r_mcangle_it4.102
r_mcbond_it2.771
r_dihedral_angle_1_deg1.269
r_angle_refined_deg1.253
r_angle_other_deg0.722
r_mcbond_other0.668
r_symmetry_hbond_refined0.265
r_nbd_other0.215
r_xyhbond_nbd_refined0.209
r_symmetry_vdw_refined0.206
r_nbd_refined0.204
r_symmetry_vdw_other0.19
r_nbtor_refined0.182
r_nbtor_other0.093
r_chiral_restr0.092
r_xyhbond_nbd_other0.075
r_bond_refined_d0.017
r_bond_other_d0.003
r_gen_planes_refined0.003
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3478
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms83

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction