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Ternary complex of Isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XGV PDB ENTRY 1XGV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 291 PEG 6K, Magnesium chloride, sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.6 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.575 α = 90 b = 107.575 β = 90 c = 171.045 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 MARRESEARCH 2003-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.089 MAX II I711
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 2.3 39.7 99.9 0.051 25.42 8.3 45289 45223 1.35 2 45.7
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 2.3 2.34 100 0.367 5.53 7.1 2259
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1XGV 2.3 39.7 1.35 45149 42860 2289 99.79 0.22722 0.2261 0.219 0.24822 0.2411 RANDOM 26.931
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] -0.3 -0.3 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.983 r_scangle_it 2.604 r_angle_refined_deg 1.928 r_scbond_it 1.668 r_mcangle_it 0.977 r_mcbond_it 0.54 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.207 r_metal_ion_refined 0.185 r_symmetry_hbond_refined 0.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.983 r_scangle_it 2.604 r_angle_refined_deg 1.928 r_scbond_it 1.668 r_mcangle_it 0.977 r_mcbond_it 0.54 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.207 r_metal_ion_refined 0.185 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6568 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing