4N54

Crystal structure of scyllo-inositol dehydrogenase from Lactobacillus casei with bound cofactor NAD(H) and scyllo-inositol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4KMXPDB ENTRY 4KMX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH7.52980.1 M magnesium chloride, 0.050 M HEPES pH 7.5, 15% w/v PEG400, 0.0125 M Tris-HCl, pH 8.0, MICROBATCH, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6453.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.25α = 90
b = 99.83β = 90
c = 192.51γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2013-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97959CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.0596.25596.90.1476.2100263100263-3-332.01
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)RedundancyNumber Unique Reflections (All)
12.052.1695.10.7770.7770.96.3

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 4KMX2.0545.6061.33100263100073499896.560.22440.22220.261149.349
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.327
f_angle_d1.329
f_chiral_restr0.105
f_bond_d0.016
f_plane_restr0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10504
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms212

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MxDCdata collection