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Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with Mg(2+), citrate and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GRI
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 3.08 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.91 α = 90 b = 104.91 β = 90 c = 146.25 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 2.65 50 99.9 22.4 9.1 27500
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 2.65 2.74
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 5GRI 2.65 45.43 26073 1382 99.73 0.1971 0.1947 0.1951 0.2414 0.2465 RANDOM 49.333
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] 3.69 3.69 -7.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.226 r_dihedral_angle_4_deg 18.568 r_dihedral_angle_3_deg 17.339 r_mcangle_it 6.877 r_dihedral_angle_1_deg 5.694 r_mcbond_it 4.709 r_mcbond_other 4.679 r_angle_refined_deg 1.347 r_angle_other_deg 1.01 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.226 r_dihedral_angle_4_deg 18.568 r_dihedral_angle_3_deg 17.339 r_mcangle_it 6.877 r_dihedral_angle_1_deg 5.694 r_mcbond_it 4.709 r_mcbond_other 4.679 r_angle_refined_deg 1.347 r_angle_other_deg 1.01 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_bond_other_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5042 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction PHASER phasing