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Crystal structure of HLA-B*07:02 with R140Q mutant IDH2 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VCL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 0.1 M Hepes pH 7.5, 0.2 M NaCl, 25% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.01 38.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.038 α = 90 b = 70.67 β = 107.39 c = 87.482 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 EIGER X 9M 2017-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.999619 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 47.43 99.2 0.068 0.074 0.999 13.57 5.973 61233 38.958
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 92.2 0.615 0.7 0.733 2.02 4.277
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 3VCL 1.9 47.43 58162 3062 99.38 0.1846 0.1819 0.1892 0.2378 0.2418 RANDOM 35.061
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] 1.15 -1.04 -0.47 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.335 r_dihedral_angle_4_deg 21.138 r_dihedral_angle_3_deg 16.267 r_dihedral_angle_1_deg 7.217 r_angle_refined_deg 1.569 r_angle_other_deg 1.34 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.335 r_dihedral_angle_4_deg 21.138 r_dihedral_angle_3_deg 16.267 r_dihedral_angle_1_deg 7.217 r_angle_refined_deg 1.569 r_angle_other_deg 1.34 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6397 Nucleic Acid Atoms Solvent Atoms 496 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling MOLREP phasing PDB_EXTRACT data extraction XDS data reduction