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Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with myo-inositol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YAB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M sodium acetate pH 4.8 - 5.4, and 12 - 35% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.2 44.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.211 α = 90 b = 120.152 β = 90 c = 140.596 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 95 CCD ADSC QUANTUM 210r 2010-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 2.3 50 98.3 0.203 7.8 3.6 64176
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 2.3 2.34 95.8 0.952 1.8 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 5YAB 2.3 49.3 60883 3208 97.96 0.19394 0.19239 0.198 0.22434 0.2321 RANDOM 28.043
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] -0.8 1.77 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.57 r_dihedral_angle_4_deg 17.547 r_dihedral_angle_3_deg 13.697 r_long_range_B_other 5.973 r_long_range_B_refined 5.972 r_dihedral_angle_1_deg 5.951 r_angle_other_deg 3.739 r_scangle_other 3.652 r_mcangle_other 2.905 r_mcangle_it 2.904
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.57 r_dihedral_angle_4_deg 17.547 r_dihedral_angle_3_deg 13.697 r_long_range_B_other 5.973 r_long_range_B_refined 5.972 r_dihedral_angle_1_deg 5.951 r_angle_other_deg 3.739 r_scangle_other 3.652 r_mcangle_other 2.905 r_mcangle_it 2.904 r_scbond_it 2.318 r_scbond_other 2.318 r_mcbond_it 1.885 r_mcbond_other 1.882 r_angle_refined_deg 1.652 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_other 0.01 r_gen_planes_refined 0.007 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11132 Nucleic Acid Atoms Solvent Atoms 419 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing