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Crystal Structure of Human IDH1 R132Q in Complex with NADPH-TCEP Adduct
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 277.15 200 mM KSCN, 24% (w/v) PEG 6000, and 5 mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.63 53.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.298 α = 90 b = 107.348 β = 99.19 c = 109.941 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 2021-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E .979180 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.16 108.53 98.01 0.992 13 3 101627 34.07
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.16 2.18 0.835
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.16 108.53 1.35 101627 5063 97.79 0.174 0.1714 0.2233 0.2141 39.75
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.8498 f_angle_d 0.8844 f_chiral_restr 0.0536 f_bond_d 0.0082 f_plane_restr 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13119 Nucleic Acid Atoms Solvent Atoms 933 Heterogen Atoms 327
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing