☰ Navigation Tabs
3D structure of E. coli Isocitrate Dehydrogenase in complex with Isocitrate, calcium(II) and thioNADP
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 = 104.01 α = 90 b = 104.01 β = 90 c = 149.563 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 MARMOSAIC 225 mm CCD MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
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 1.8 50 99.4 0.07 17.7 7.2 76263 -3 24.08
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 1.8 1.91 96.7 0.63 2.7 7.2
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 1.799 46.515 2.01 76173 3802 99.45 0.1843 0.1833 0.1826 0.204 0.2038
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] -0.565 -0.565 -10.1539
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.35 f_angle_d 1.086 f_chiral_restr 0.075 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3205 Nucleic Acid Atoms Solvent Atoms 507 Heterogen Atoms 67
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing