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Structure of 2Q1-Fab, an antibody selective for IDH2R140Q-HLA-B*07:02
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UJ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M Bis-Tris pH 5.5, 25% (w/v) PEG 3350, 0.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.44 49.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.462 α = 90 b = 263.955 β = 99.53 c = 91.237 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 277 PIXEL DECTRIS EIGER X 9M 2019-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON OTHER 0.92009
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 2.4 45.53 98.7 0.096 0.118 0.993 8.82 2.866 68740 38.118
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 2.4 2.46 98.8 0.468 0.592 0.676 2.08 2.627
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 6UJ9 2.4 45.53 65303 3437 98.77 0.2111 0.2081 0.213 0.2686 0.2711 RANDOM 39.047
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] 0.56 0.01 0.5 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.554 r_dihedral_angle_4_deg 23.205 r_dihedral_angle_3_deg 15.935 r_dihedral_angle_1_deg 8.248 r_angle_refined_deg 1.812 r_angle_other_deg 1.35 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.554 r_dihedral_angle_4_deg 23.205 r_dihedral_angle_3_deg 15.935 r_dihedral_angle_1_deg 8.248 r_angle_refined_deg 1.812 r_angle_other_deg 1.35 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12900 Nucleic Acid Atoms Solvent Atoms 595 Heterogen Atoms 261
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction