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Human Class I MHC HLA-A2 in complex with the nonameric Melan-A/MART-1(27-35) peptide having A28L substitution
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 PEG 3350 24%, MES 0.025M, NH4Cl 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.32 47.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.4 α = 90 b = 84.31 β = 90.13 c = 84.14 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 2005-11-22 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 97 0.1 13.1 3.5 90210 87504 1 16.7
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 85.6 0.479 2.1 2.6 7671
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 1TVB 1.7 20 1 90185 83098 4382 96.95 0.17412 0.17412 0.17184 0.1737 0.2173 0.22 RANDOM 21.719
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] -0.69 0.17 1.6 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.731 r_dihedral_angle_4_deg 20.887 r_dihedral_angle_3_deg 14.818 r_dihedral_angle_1_deg 6.135 r_scangle_it 4.624 r_scbond_it 2.882 r_angle_refined_deg 1.71 r_mcangle_it 1.701 r_mcbond_it 0.939 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.731 r_dihedral_angle_4_deg 20.887 r_dihedral_angle_3_deg 14.818 r_dihedral_angle_1_deg 6.135 r_scangle_it 4.624 r_scbond_it 2.882 r_angle_refined_deg 1.71 r_mcangle_it 1.701 r_mcbond_it 0.939 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.199 r_metal_ion_refined 0.192 r_xyhbond_nbd_refined 0.189 r_nbd_refined 0.162 r_chiral_restr 0.154 r_symmetry_vdw_refined 0.124 r_bond_refined_d 0.016 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6288 Nucleic Acid Atoms Solvent Atoms 812 Heterogen Atoms 38
Software Software Software Name Purpose Blu-Ice data collection HKL-2000 data reduction MOLREP phasing REFMAC refinement HKL-2000 data scaling