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Crystal structure of HLA-B*07:02 with wild-type IDH2 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UJ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 0.1 M MES pH 6.5, 0.2 M KI, 30% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.03 39.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.69 α = 90 b = 70.48 β = 107.65 c = 88.146 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 16M 2017-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979321 NSLS-II 17-ID-2
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 2.25 47.58 99.7 0.096 0.107 0.996 10.44 5.078 37664 46.168
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 2.25 2.31 99.7 0.655 0.735 0.766 2.13 4.66
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 6UJ7 2.25 47.58 35786 1884 99.82 0.2179 0.2156 0.2233 0.2599 0.2655 RANDOM 42.004
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] 0.2 -0.49 -0.56 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.861 r_dihedral_angle_4_deg 19.484 r_dihedral_angle_3_deg 17.965 r_dihedral_angle_1_deg 5.994 r_angle_refined_deg 1.532 r_angle_other_deg 1.324 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.861 r_dihedral_angle_4_deg 19.484 r_dihedral_angle_3_deg 17.965 r_dihedral_angle_1_deg 5.994 r_angle_refined_deg 1.532 r_angle_other_deg 1.324 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6354 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 96
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction