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Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP, isocitrate, and calcium(2+)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LWD PDB ENTRY 1LWD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.9 293 PEG 6000, MES, NADP, isocitrate, calcium chloride, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.65 53.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.298 α = 90 b = 86.738 β = 107.15 c = 115.766 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 100 IMAGE PLATE RIGAKU RAXIS IV confocal mirror 2003-12-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU ULTRAX 18 1.5418
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 2.41 12 95.7 0.085 7.8 3.1 71234 71234 26.1
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) 2.41 2.5 95.7 0.085 2.9 2.9 6671
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 1LWD 2.41 12 70684 70684 3622 94.2 0.214 0.214 0.2159 0.253 0.2123 RANDOM 23.7
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] -3.72 1.25 3.25 0.47
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.1 c_angle_deg 1.3 c_improper_angle_d 0.77 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13124 Nucleic Acid Atoms Solvent Atoms 914 Heterogen Atoms 248
Software Software Software Name Purpose CNS refinement CrystalClear data reduction CrystalClear data scaling CNS phasing