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Human Class I MHC HLA-A2 in complex with the native nonameric Melan-A/MART-1(27-35) peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TVB PDB entry 1TVB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 PEG3350 24%, MES 0.025M, NaCl 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.32 46.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.957 α = 90 b = 58.369 β = 109.66 c = 89.425 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 300 mm CCD 2005-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 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 1.9 20 96.4 0.107 14.2 3 65376 63002 1 1 15.6
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 1.9 1.97 87.9 0.463 2.5 2.4 5674
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 (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 1TVB 1.9 20 1 65370 59801 3183 96.35 0.19022 0.18733 0.1873 0.24427 0.2433 RANDOM 15.408
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] 0.47 0.6 -1.73 1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.283 r_dihedral_angle_3_deg 17.108 r_dihedral_angle_4_deg 15.936 r_dihedral_angle_1_deg 6.538 r_scangle_it 4.912 r_scbond_it 3.097 r_mcangle_it 1.842 r_angle_refined_deg 1.764 r_mcbond_it 0.992 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.283 r_dihedral_angle_3_deg 17.108 r_dihedral_angle_4_deg 15.936 r_dihedral_angle_1_deg 6.538 r_scangle_it 4.912 r_scbond_it 3.097 r_mcangle_it 1.842 r_angle_refined_deg 1.764 r_mcbond_it 0.992 r_nbtor_refined 0.314 r_xyhbond_nbd_refined 0.206 r_symmetry_hbond_refined 0.196 r_nbd_refined 0.157 r_chiral_restr 0.137 r_metal_ion_refined 0.133 r_symmetry_vdw_refined 0.113 r_bond_refined_d 0.017 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6282 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection HKL-2000 data scaling MOLREP phasing