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Human Class I MHC HLA-A2 in complex with the modified HTLV-1 TAX (Y5K-4-[3-Indolyl]-butyric acid) peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AV1 PDB ENTRY 2AV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 PEG3350 24%, MES 0.025M, HCOOH 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.5 50.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.384 α = 82 b = 62.709 β = 76.22 c = 74.773 γ = 78.18
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 MARMOSAIC 300 mm CCD 2005-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.979 APS 23-ID-D
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 1.7 20 91.8 0.087 14 1.9 94809 87035 1 1 18
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 1.7 1.76 66.2 0.239 3.13 1.7 6273
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 2AV1 1.7 20 1 95058 82640 4395 91.56 0.18191 0.18191 0.17985 0.1813 0.21947 0.2227 RANDOM; 5% of the data set 11.513
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] 1.93 0.47 0.66 -1.11 0.47 -1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.237 r_dihedral_angle_4_deg 19.12 r_dihedral_angle_3_deg 14.733 r_dihedral_angle_1_deg 6.356 r_scangle_it 4.333 r_scbond_it 2.771 r_angle_refined_deg 1.729 r_mcangle_it 1.664 r_mcbond_it 0.947 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.237 r_dihedral_angle_4_deg 19.12 r_dihedral_angle_3_deg 14.733 r_dihedral_angle_1_deg 6.356 r_scangle_it 4.333 r_scbond_it 2.771 r_angle_refined_deg 1.729 r_mcangle_it 1.664 r_mcbond_it 0.947 r_nbtor_refined 0.311 r_xyhbond_nbd_refined 0.205 r_symmetry_hbond_refined 0.181 r_nbd_refined 0.155 r_chiral_restr 0.142 r_metal_ion_refined 0.123 r_symmetry_vdw_refined 0.109 r_bond_refined_d 0.016 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6313 Nucleic Acid Atoms Solvent Atoms 788 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data scaling MOLREP phasing