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Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with Mg(2+) and citrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GRH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.2 M sodium citrate, pH 8.0, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.48 64.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.04 α = 90 b = 112.04 β = 90 c = 144.95 γ = 120
Symmetry Space Group P 31 2 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 PILATUS3 6M 2015-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 1.0000 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.3 50 98.4 53.7 19.5 46471
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38
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 5GRH 2.31 46.01 40334 2138 90.4 0.2424 0.2409 0.2426 0.2712 0.2737 RANDOM 44.364
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] 2.09 2.09 -4.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.917 r_dihedral_angle_4_deg 21.152 r_dihedral_angle_3_deg 16.624 r_dihedral_angle_1_deg 5.443 r_angle_refined_deg 0.987 r_angle_other_deg 0.755 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_bond_other_d 0.005 r_gen_planes_refined 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.917 r_dihedral_angle_4_deg 21.152 r_dihedral_angle_3_deg 16.624 r_dihedral_angle_1_deg 5.443 r_angle_refined_deg 0.987 r_angle_other_deg 0.755 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_bond_other_d 0.005 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5039 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data processing PHASER phasing