2IAM

Structural basis for recognition of mutant self by a tumor-specific, MHC class II-restricted TCR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FYT1FYT, 1IAL
experimental modelPDB 1IAL1FYT, 1IAL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52958% PEG6000, 0.1M di-ammonium phosphate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.0259.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.391α = 90
b = 270.542β = 90
c = 97.396γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2005-08-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.85092.80.09110.726581
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.82.9491.90.51335639

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1FYT, 1IAL2.841.912637525046132992.160.210510.206930.27915RANDOM62.8
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]
-5.394.950.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.547
r_dihedral_angle_3_deg21.109
r_dihedral_angle_4_deg18.69
r_dihedral_angle_1_deg10.92
r_scangle_it2.944
r_angle_refined_deg1.96
r_scbond_it1.908
r_mcangle_it1.278
r_mcbond_it0.752
r_nbtor_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.547
r_dihedral_angle_3_deg21.109
r_dihedral_angle_4_deg18.69
r_dihedral_angle_1_deg10.92
r_scangle_it2.944
r_angle_refined_deg1.96
r_scbond_it1.908
r_mcangle_it1.278
r_mcbond_it0.752
r_nbtor_refined0.322
r_symmetry_vdw_refined0.256
r_nbd_refined0.253
r_xyhbond_nbd_refined0.178
r_chiral_restr0.117
r_symmetry_hbond_refined0.043
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6511
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
PHASERphasing