5YA8

Crystal structure of scyllo-inositol dehydrogenase with L-glucose dehydrogenase activity complexed with myo-inositol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5YAB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M sodium acetate pH 4.8 - 5.4, and 12 - 35% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.244.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.211α = 90
b = 120.152β = 90
c = 140.596γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 210r2010-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0000Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.35098.30.2037.83.664176
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3495.80.9521.83.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5YAB2.349.360883320897.960.193940.192390.22434RANDOM28.043
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]
-0.81.77-0.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.57
r_dihedral_angle_4_deg17.547
r_dihedral_angle_3_deg13.697
r_long_range_B_other5.973
r_long_range_B_refined5.972
r_dihedral_angle_1_deg5.951
r_angle_other_deg3.739
r_scangle_other3.652
r_mcangle_other2.905
r_mcangle_it2.904
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.57
r_dihedral_angle_4_deg17.547
r_dihedral_angle_3_deg13.697
r_long_range_B_other5.973
r_long_range_B_refined5.972
r_dihedral_angle_1_deg5.951
r_angle_other_deg3.739
r_scangle_other3.652
r_mcangle_other2.905
r_mcangle_it2.904
r_scbond_it2.318
r_scbond_other2.318
r_mcbond_it1.885
r_mcbond_other1.882
r_angle_refined_deg1.652
r_chiral_restr0.09
r_bond_refined_d0.014
r_gen_planes_other0.01
r_gen_planes_refined0.007
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 AtomsNumber
Protein Atoms11132
Nucleic Acid Atoms
Solvent Atoms419
Heterogen Atoms212

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing