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3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with isocitrate and magnesium(II)
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 5.8 A SOLUTION OF THE LYS100MET MUTANT (20 MG/ML PROTEIN IN 0.9 MM CITRIC ACID, 3.5 MM NA2HPO4 PH 6.0, 100 MM NACL, 0.02% NAN3 AND 2 MM DTT) WAS MIXED 1:1 WITH A CRYSTALLIZATION SOLUTION (1.85 M NH4SO4, 50 MM CITRIC ACID/NA2HPO4, 0.1 M NACL AND 0.2 M DTT AT PH 5.8) AND 2 UL DROPS EQUILIBRATED AGAINST 500 UL OF THE CRYSTALLIZATION SOLUTION. TETRAGONAL BIPYRAMIDAL CRYSTALS, 300 UM X 150 UM X 75 UM, DEVELOPED WITHIN 5 DAYS.
Crystal Properties Matthews coefficient Solvent content 4.5 72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.562 α = 90 b = 102.562 β = 90 c = 150.645 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 PROTEUM X8 PT135 2008-06-16 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 2 52.2 100 0.08 14.5 5.6 55032 19.11
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 2.1 100 0.36 3.1 4.3
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1AI2 2 51.281 54942 2773 99.98 0.1645 0.1631 0.1612 0.1915 0.1873
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.968 f_angle_d 1.027 f_chiral_restr 0.072 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3204 Nucleic Acid Atoms Solvent Atoms 526 Heterogen Atoms 19
Software Software Software Name Purpose PHENIX refinement SAINT data reduction SADABS data scaling PHASER phasing