2GJ6

The complex between TCR A6 and human Class I MHC HLA-A2 with the modified HTLV-1 TAX (Y5K-4-[3-Indolyl]-butyric acid) peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QSEPDB ENTRY 1QSE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5297PEG8000 30%, 0.1 M Sodium Cacodylate, 0.2 M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.7455.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 223.846α = 90
b = 49.019β = 90.34
c = 94.17γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCUSTOM-MADE2005-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9829APS19-BM

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
12.56200.9920.09215.43.532172319151153
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)
12.562.7193.10.4732.22.92960

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTPDB ENTRY 1QSE2.562013335430313160095.680.202070.199490.24988RANDOM; 5% of the data set44.495
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]
-3.43-0.583.87-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.383
r_dihedral_angle_3_deg20.674
r_dihedral_angle_4_deg20.061
r_dihedral_angle_1_deg7.333
r_scangle_it2.486
r_angle_refined_deg1.676
r_scbond_it1.586
r_mcangle_it0.985
r_mcbond_it0.565
r_nbtor_refined0.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.383
r_dihedral_angle_3_deg20.674
r_dihedral_angle_4_deg20.061
r_dihedral_angle_1_deg7.333
r_scangle_it2.486
r_angle_refined_deg1.676
r_scbond_it1.586
r_mcangle_it0.985
r_mcbond_it0.565
r_nbtor_refined0.321
r_xyhbond_nbd_refined0.198
r_symmetry_hbond_refined0.159
r_nbd_refined0.128
r_chiral_restr0.121
r_symmetry_vdw_refined0.107
r_bond_refined_d0.014
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6625
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms117

Software

Software
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
HKL-2000data scaling
MOLREPphasing