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Crystal Structure of apo myo-inositol dehydrogenase from Lactobacillus casei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MZ0 PDB ENTRY 3MZ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 298 ammonium sulfate, pH 6.5, MICROBATCH, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.41 49.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.11 α = 90 b = 110.98 β = 90 c = 125.65 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 2011-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 0.97952 CLSI 08B1-1
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 83.18 99.9 0.104 13.2 6.9 101470 101470 24.97
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 2.11 99.6 0.597 0.597 1.2 6.2 14603
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3MZ0 2 41.59 1.36 101501 101397 5066 99.83 0.191 0.1886 0.1917 0.2288 0.2316 RANDOM 25.7928
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 14.657 f_angle_d 1.128 f_chiral_restr 0.108 f_bond_d 0.018 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10528 Nucleic Acid Atoms Solvent Atoms 694 Heterogen Atoms 102
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction MxDC data collection