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Crystal structure of Saccharomyces cerevesiae mitochondrial NADP(+)-dependent isocitrate dehydrogenase in complex with isocitrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LWD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 0.1M HEPES-Na, 0.2M Li2SO4, 0.1M NaF, 20% PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.38 48.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.699 α = 90 b = 97.886 β = 98.95 c = 190.651 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 IMAGE PLATE RIGAKU RAXIS IV++ MSC confocal max-flux optics 2005-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.6 19.9 98.4 0.06 0.06 9 2.62 82166 64.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 99.9 0.228 0.06 2 2.66 8296
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 1LWD 2.6 20 82147 4154 98.38 0.235 0.232 0.2484 0.292 0.2475 RANDOM 51.646
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] 1.39 -2.13 -0.79 -1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 3.941 r_scangle_it 2.166 r_mcangle_it 1.319 r_scbond_it 1.192 r_angle_refined_deg 0.89 r_mcbond_it 0.693 r_nbd_refined 0.187 r_symmetry_vdw_refined 0.159 r_xyhbond_nbd_refined 0.107 r_symmetry_hbond_refined 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 3.941 r_scangle_it 2.166 r_mcangle_it 1.319 r_scbond_it 1.192 r_angle_refined_deg 0.89 r_mcbond_it 0.693 r_nbd_refined 0.187 r_symmetry_vdw_refined 0.159 r_xyhbond_nbd_refined 0.107 r_symmetry_hbond_refined 0.099 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19452 Nucleic Acid Atoms Solvent Atoms 1158 Heterogen Atoms 78
Software Software Software Name Purpose d*TREK data scaling CNS refinement REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection CrystalClear data reduction CNS phasing