☰ Navigation Tabs
Human Class I MHC HLA-A2 in complex with the nonameric Melan-A/MART-1(27-35) peptide having A27L 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, HCOOK 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.32 47.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.309 α = 90 b = 84.271 β = 90.11 c = 84.293 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 2005-08-20 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 1.548 20 93.2 0.108 14.8 3.1 118490 110421 1 1 17
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 1.548 1.61 71.2 0.354 2.11 1.5 8400
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 1.548 20 1 118485 104852 5541 93.17 0.18317 0.18317 0.18135 0.1843 0.21768 0.2197 RANDOM 22.072
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] -0.84 0.39 1.08 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.491 r_dihedral_angle_4_deg 19.177 r_dihedral_angle_3_deg 15.348 r_dihedral_angle_1_deg 6.205 r_scangle_it 4.882 r_scbond_it 3.035 r_mcangle_it 1.884 r_angle_refined_deg 1.73 r_mcbond_it 1.065 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.491 r_dihedral_angle_4_deg 19.177 r_dihedral_angle_3_deg 15.348 r_dihedral_angle_1_deg 6.205 r_scangle_it 4.882 r_scbond_it 3.035 r_mcangle_it 1.884 r_angle_refined_deg 1.73 r_mcbond_it 1.065 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.212 r_xyhbond_nbd_refined 0.184 r_nbd_refined 0.164 r_chiral_restr 0.158 r_symmetry_vdw_refined 0.139 r_metal_ion_refined 0.081 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 672 Heterogen Atoms 44
Software Software Software Name Purpose Blu-Ice data collection HKL-2000 data reduction MOLREP phasing REFMAC refinement HKL-2000 data scaling