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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.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DUZ PDB Entry 1DUZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 PEG3350 20%, MES 0.025M, NaSCN 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.5 49.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.328 α = 82.1 b = 62.536 β = 76.39 c = 74.747 γ = 78.1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD CUSTOM-MADE 2004-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97951 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.95 20 96.4 0.072 10.29 1.9 63772 61476 1 1 17.73
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 91.2 0.302 2.22 1.7 5799
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB Entry 1DUZ 1.95 10 1 62423 57226 3050 96.56 0.17724 0.17724 0.17441 0.175 0.23059 0.2323 RANDOM 12.902
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 -0.06 0.44 -0.79 0.45 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.557 r_scangle_it 4.62 r_scbond_it 3.113 r_angle_refined_deg 2.048 r_mcangle_it 1.766 r_mcbond_it 1.053 r_symmetry_hbond_refined 0.221 r_xyhbond_nbd_refined 0.217 r_symmetry_vdw_refined 0.192 r_nbd_refined 0.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.557 r_scangle_it 4.62 r_scbond_it 3.113 r_angle_refined_deg 2.048 r_mcangle_it 1.766 r_mcbond_it 1.053 r_symmetry_hbond_refined 0.221 r_xyhbond_nbd_refined 0.217 r_symmetry_vdw_refined 0.192 r_nbd_refined 0.165 r_chiral_restr 0.142 r_bond_refined_d 0.021 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6314 Nucleic Acid Atoms Solvent Atoms 751 Heterogen Atoms 141
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing