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Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase R132H mutant in complex with NADPH, ALPHA-KETOGLUTARATE and CALCIUM(2+)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T0L PDB ENTRY 1T0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Protein component: 8 mg/ml IDH, 20mM Tris-HCl pH 7.5, 100mM sodium chloride,
10mM NADPH, 10mM calcium chloride, 75mM alpha-ketoglutaric acid sodium salt.
Precipitant: 100mM MES pH 6.5, 20% PEG 6000. Ratio of protein component to
precipitant in initial hanging drop: 2:1., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.67 53.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.12 α = 90 b = 274.69 β = 90 c = 116.5 γ = 90
Symmetry Space Group C 2 2 21
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 315r MIRROR AND MONOCHROMETER 2009-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0809 NSLS X29A
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 2.1 25 92.4 0.08 20.3 8.6 89958 83121 31
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 2.1 2.18 58.8 0.305 2.4 2.1 5232
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1T0L 2.1 24.91 83109 78956 4153 92.36 0.222 0.22 0.2149 0.262 0.2511 RANDOM 33.273
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] 0.03 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.825 r_dihedral_angle_4_deg 25.226 r_dihedral_angle_3_deg 19.723 r_dihedral_angle_1_deg 6.858 r_scangle_it 3.774 r_scbond_it 2.321 r_mcangle_it 1.318 r_angle_refined_deg 1.105 r_mcbond_it 0.698 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.825 r_dihedral_angle_4_deg 25.226 r_dihedral_angle_3_deg 19.723 r_dihedral_angle_1_deg 6.858 r_scangle_it 3.774 r_scbond_it 2.321 r_mcangle_it 1.318 r_angle_refined_deg 1.105 r_mcbond_it 0.698 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9706 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 198
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection