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Crystal structure of scyllo-inositol dehydrogenase from Lactobacillus casei with bound cofactor NAD(H) and scyllo-inositol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KMX PDB ENTRY 4KMX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 298 0.1 M magnesium chloride, 0.050 M HEPES pH 7.5, 15% w/v PEG400, 0.0125 M Tris-HCl, pH 8.0, MICROBATCH, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.64 53.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.25 α = 90 b = 99.83 β = 90 c = 192.51 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX300HE 2013-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97959 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.05 96.255 96.9 0.14 7 6.2 100263 100263 -3 -3 32.01
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.16 95.1 0.777 0.777 0.9 6.3
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 4KMX 2.05 45.606 1.33 100263 100073 4998 96.56 0.2244 0.2222 0.2239 0.2611 0.263 49.349
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 15.327 f_angle_d 1.329 f_chiral_restr 0.105 f_bond_d 0.016 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10504 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 212
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction MxDC data collection