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Crystal structure of myo-inositol dehydrogenase from Bacillus subtilis with bound cofactor and product inosose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MZ0 PDB ENTRY 3MZ0 (apo-IDH)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.4 298 0.1M tri-sodium citrate pH 5.4, 2.6M ammonium sulfate, microbatch, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.35 63.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.498 α = 90 b = 183.498 β = 90 c = 183.498 γ = 90
Symmetry Space Group I 21 3
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 2009-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97934 CLSI 08ID-1
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 2.8 39.122 100 0.13 8.2 22.38 25421 80
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) 2.8 2.9 100 0.905 1.3 22.8 2540
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3MZ0 (apo-IDH) 2.9006 39.122 1.36 22866 1170 99.93 0.2434 0.2408 0.2405 0.2912 0.2878 RANDOM 111.7268
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 20.076 f_angle_d 1.335 f_chiral_restr 0.08 f_bond_d 0.01 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5280 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 112
Software Software Software Name Purpose d*TREK data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction MxDC data collection d*TREK data reduction