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Structure of HLA-A2 in complex with an altered peptide ligands based on Mart-1 variant epitope
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X70
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 295 Good diffracting crystals were obtained by streak seeding
Crystal Properties Matthews coefficient Solvent content 2.45 49.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.18 α = 90 b = 87.14 β = 90.15 c = 79.194 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 PIXEL DECTRIS PILATUS 2M 2012-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.9789 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.65 79.194 99.6 0.041 0.049 0.026 17 3.4 102600 102600
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.74 99.8 0.483 0.483 0.301 1.6 3.5 14976
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2X70 1.65 19.94 5093 98.76 0.1564 0.1553 0.1764 0.1787 0.2032 RANDOM 27.234
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] -3.89 -0.73 12.12 -8.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.022 r_dihedral_angle_4_deg 17.902 r_dihedral_angle_3_deg 12.901 r_dihedral_angle_1_deg 6.16 r_mcangle_it 2.685 r_mcbond_it 2.016 r_mcbond_other 2.013 r_angle_refined_deg 1.687 r_angle_other_deg 1.406 r_chiral_restr 0.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.022 r_dihedral_angle_4_deg 17.902 r_dihedral_angle_3_deg 12.901 r_dihedral_angle_1_deg 6.16 r_mcangle_it 2.685 r_mcbond_it 2.016 r_mcbond_other 2.013 r_angle_refined_deg 1.687 r_angle_other_deg 1.406 r_chiral_restr 0.243 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6308 Nucleic Acid Atoms Solvent Atoms 536 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement SCALA data scaling XDS data reduction PDB_EXTRACT data extraction AMoRE phasing