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Crystal structure of human IDH1 in complex with GSK321A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L04 PDB entry 4L04
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 18-23% PEG3350, 0.2M ammonium sulfate, 0.1M Bis-Tris, pH 7.0, 10mM NADP+
Crystal Properties Matthews coefficient Solvent content 2.79 55.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.726 α = 90 b = 82.726 β = 90 c = 303.639 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2014-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97856 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.25 30 99.9 0.067 10.1 8.5 51200
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.33 100 0.713 8.6 5005
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 4L04 2.25 29.93 48511 2589 99.88 0.2222 0.2203 0.2215 0.2579 0.2591 RANDOM 50.448
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] 0.5 0.5 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.947 r_dihedral_angle_4_deg 17.6 r_dihedral_angle_3_deg 11.538 r_dihedral_angle_1_deg 5.079 r_mcangle_it 1.659 r_angle_refined_deg 0.951 r_mcbond_it 0.931 r_mcbond_other 0.931 r_angle_other_deg 0.659 r_chiral_restr 0.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.947 r_dihedral_angle_4_deg 17.6 r_dihedral_angle_3_deg 11.538 r_dihedral_angle_1_deg 5.079 r_mcangle_it 1.659 r_angle_refined_deg 0.951 r_mcbond_it 0.931 r_mcbond_other 0.931 r_angle_other_deg 0.659 r_chiral_restr 0.049 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6235 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 170
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing