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Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with L-glucono-1,5-lactone
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, 12 - 35% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.24 45.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.571 α = 90 b = 121.177 β = 90 c = 140.865 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 1.000 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 1.8 50 99.6 0.082 18.1 3.6 137356
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 1.8 1.83 99 0.619 2.3 3.4
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 1.8 31.5 130434 6847 99.39 0.16295 0.16255 0.1735 0.17045 0.1812 RANDOM 19.653
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] -0.59 1.03 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.428 r_dihedral_angle_4_deg 18.366 r_dihedral_angle_3_deg 13.179 r_dihedral_angle_1_deg 6.056 r_long_range_B_refined 4.657 r_long_range_B_other 4.657 r_scangle_other 2.754 r_mcangle_it 1.75 r_mcangle_other 1.75 r_scbond_it 1.697
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.428 r_dihedral_angle_4_deg 18.366 r_dihedral_angle_3_deg 13.179 r_dihedral_angle_1_deg 6.056 r_long_range_B_refined 4.657 r_long_range_B_other 4.657 r_scangle_other 2.754 r_mcangle_it 1.75 r_mcangle_other 1.75 r_scbond_it 1.697 r_scbond_other 1.697 r_angle_refined_deg 1.486 r_mcbond_it 1.105 r_mcbond_other 1.103 r_angle_other_deg 0.982 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.002 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 11118 Nucleic Acid Atoms Solvent Atoms 853 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing