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Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Listeria monocytogenes in the complex with IMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PVN PDBID 1PVN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 289 0.2 M ammonium formate pH 6.6, 20 % (w/v) PEG
Crystal Properties Matthews coefficient Solvent content 2.3 46.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.977 α = 111.36 b = 95.699 β = 105.17 c = 97.604 γ = 107.61
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 X 6M 2014-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97915 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.5 50 97.7 0.056 0.051 13.11 2.2 78331 34.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 88.6 0.426 0.784 1.71 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 FREE R-VALUE PDBID 1PVN 2.5 39.88 1.98 67381 3344 83.54 0.1961 0.194 0.1938 0.2386 0.2386 42.68
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 13.6468 f_angle_d 0.4274 f_chiral_restr 0.0407 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15775 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 150
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing MLPHARE phasing Coot model building