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Crystal structure of HTLV-1 TAX peptide Bound to Human Class I MHC HLA-A2 with the K66A mutation 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 24%, MES 0.025M., 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 = 50.32 α = 82.13 b = 62.532 β = 76.57 c = 74.801 γ = 78.06
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 2004-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97925 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 2.05 20 95.5 0.075 10.5 1.9 56534 53990 1 1 19.9
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 2.05 2.12 83.7 0.28 2.34 1.7 4763
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 2.05 10 1 53796 49005 2612 95.95 0.17472 0.17472 0.17149 0.1728 0.23408 0.234 RANDOM 14.881
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] 1.5 0.32 0.36 -0.78 0.19 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.63 r_scangle_it 4.352 r_scbond_it 2.939 r_angle_refined_deg 1.943 r_mcangle_it 1.695 r_mcbond_it 0.962 r_symmetry_hbond_refined 0.219 r_xyhbond_nbd_refined 0.21 r_nbd_refined 0.157 r_chiral_restr 0.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.63 r_scangle_it 4.352 r_scbond_it 2.939 r_angle_refined_deg 1.943 r_mcangle_it 1.695 r_mcbond_it 0.962 r_symmetry_hbond_refined 0.219 r_xyhbond_nbd_refined 0.21 r_nbd_refined 0.157 r_chiral_restr 0.143 r_symmetry_vdw_refined 0.13 r_bond_refined_d 0.02 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6314 Nucleic Acid Atoms Solvent Atoms 695 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing