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Crystal structure of isocitrate dehydrogenase from Ostreococcus tauri in complex with isocitrate and magnesium(II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IXL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 286 20% PEG 4000, 10% 2-propanol, 0.1 M sodium citrate (pH 5.5).
Crystal Properties Matthews coefficient Solvent content 2.77 55.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.25 α = 89.15 b = 78.511 β = 103.59 c = 111.056 γ = 111.89
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 2015-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97915 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.8 20 94.9 0.039 0.998 14.4 2.2 177015
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 0.84
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 6IXL 1.8 19.95 168180 8824 94.9 0.2095 0.208 0.2151 0.2392 0.2439 RANDOM 29.875
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] -0.21 -0.56 1.74 -0.46 0.24 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.471 r_dihedral_angle_4_deg 20.512 r_dihedral_angle_3_deg 16.21 r_dihedral_angle_1_deg 5.585 r_angle_other_deg 1.563 r_angle_refined_deg 1.519 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.471 r_dihedral_angle_4_deg 20.512 r_dihedral_angle_3_deg 16.21 r_dihedral_angle_1_deg 5.585 r_angle_other_deg 1.563 r_angle_refined_deg 1.519 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12288 Nucleic Acid Atoms Solvent Atoms 693 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction