2AV1

Crystal structure of HTLV-1 TAX peptide Bound to Human Class I MHC HLA-A2 with the E63Q and K66A mutations in the heavy chain.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DUZPDB Entry 1DUZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5277PEG3350 20%, MES 0.025M, NaSCN 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.549.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.328α = 82.1
b = 62.536β = 76.39
c = 74.747γ = 78.1
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCUSTOM-MADE2004-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97951APS19-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
11.952096.40.07210.291.963772614761117.73
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)
11.952.0291.20.3022.221.75799

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB Entry 1DUZ1.951016242357226305096.560.177240.177240.174410.23059RANDOM12.902
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]
0.99-0.060.44-0.790.45-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.557
r_scangle_it4.62
r_scbond_it3.113
r_angle_refined_deg2.048
r_mcangle_it1.766
r_mcbond_it1.053
r_symmetry_hbond_refined0.221
r_xyhbond_nbd_refined0.217
r_symmetry_vdw_refined0.192
r_nbd_refined0.165
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.557
r_scangle_it4.62
r_scbond_it3.113
r_angle_refined_deg2.048
r_mcangle_it1.766
r_mcbond_it1.053
r_symmetry_hbond_refined0.221
r_xyhbond_nbd_refined0.217
r_symmetry_vdw_refined0.192
r_nbd_refined0.165
r_chiral_restr0.142
r_bond_refined_d0.021
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6314
Nucleic Acid Atoms
Solvent Atoms751
Heterogen Atoms141

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing