☰ Navigation Tabs
Crystal structure of the alpha gamma mutant (gamma-K151A) 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 3.6 65.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.336 α = 90 b = 114.336 β = 90 c = 143.901 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 0.97915 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 2.5 50 99.9 23.4 4.9 38210
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 2.5 2.59
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 2.5 49.51 36284 1889 99.87 0.2088 0.2069 0.2092 0.2475 0.2471 RANDOM 68.322
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] 28.29 28.29 -56.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.411 r_dihedral_angle_4_deg 17.126 r_dihedral_angle_3_deg 16.247 r_mcangle_it 8.558 r_mcbond_it 6.206 r_mcbond_other 6.199 r_dihedral_angle_1_deg 5.936 r_angle_refined_deg 1.257 r_angle_other_deg 0.936 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.411 r_dihedral_angle_4_deg 17.126 r_dihedral_angle_3_deg 16.247 r_mcangle_it 8.558 r_mcbond_it 6.206 r_mcbond_other 6.199 r_dihedral_angle_1_deg 5.936 r_angle_refined_deg 1.257 r_angle_other_deg 0.936 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_bond_other_d 0.006 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5046 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction PHASER phasing