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3D structure of E. coli Isocitrate Dehydrogenase in complex with Isocitrate, calcium(II) and NADP - The pseudo-Michaelis complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AI2 PDB ENTRY 1AI2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 1.85 M NH4SO4, 50 MM CITRIC ACID/NA2HPO4 BUFFER PH 5.8, 0.1 M NACL AND 0.2 M DTT
Crystal Properties Matthews coefficient Solvent content 4.5 72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.297 α = 90 b = 105.297 β = 90 c = 145.723 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 BRUKER AXS PT135 MONTEL MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR
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 1.9 47.1 99.9 0.11 11.2 5.7 65181 19.9
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 1.9 2 100 0.54 1.7 3.4
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1AI2 1.9 44.809 1.33 65078 3272 99.94 0.1904 0.1886 0.1866 0.224 0.2203
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] -5.8691 -5.8691 -11.241
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.554 f_angle_d 1.088 f_chiral_restr 0.07 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3210 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement SAINT data reduction SADABS data scaling PHASER phasing