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Crystal Structure of Human IDH1 R132Q in complex with NADPH and Alpha-Ketoglutarate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KZO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 277.15 160mM NaNO3 and 20% W/V PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.42 49.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.821 α = 90 b = 104.86 β = 98.19 c = 107.711 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 EIGER2 X 16M 2022-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 .97946 SSRL BL12-1
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 2.28 39.15 98.28 0.997 10.65 2 82740 35.61
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 2.28 2.36 0.748
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.28 39.15 1.34 82740 4053 98.16 0.1701 0.1673 0.1676 0.2223 0.2222
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 8.539 f_angle_d 0.923 f_chiral_restr 0.054 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13053 Nucleic Acid Atoms Solvent Atoms 462 Heterogen Atoms 228
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing