3PWP

The complex between TCR A6 and human Class I MHC HLA-A2 with the bound HuD peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AO7PDB entry 1AO7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529830% PEG3350, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7354.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 224.006α = 90
b = 49.065β = 90.07
c = 93.711γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.98APS31-ID

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
12.692094.40.078173.628642270381161.8
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)
2.692.7563.20.372.7910

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1AO72.69202870227035137194.190.20090.20090.19790.2587RANDOM, 5%55.0952
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]
-4.171.275-0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.92
r_dihedral_angle_3_deg21.336
r_dihedral_angle_4_deg18.465
r_dihedral_angle_1_deg7.611
r_angle_refined_deg1.69
r_mcangle_it1.588
r_scangle_it1.4
r_mcbond_it0.943
r_scbond_it0.874
r_nbtor_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.92
r_dihedral_angle_3_deg21.336
r_dihedral_angle_4_deg18.465
r_dihedral_angle_1_deg7.611
r_angle_refined_deg1.69
r_mcangle_it1.588
r_scangle_it1.4
r_mcbond_it0.943
r_scbond_it0.874
r_nbtor_refined0.323
r_symmetry_hbond_refined0.269
r_xyhbond_nbd_refined0.209
r_nbd_refined0.131
r_chiral_restr0.121
r_symmetry_vdw_refined0.108
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6638
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms47

Software

Software
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SGX-CATdata collection
HKL-2000data reduction
HKL-2000data scaling