4MTJ

Structure of the b12-independent glycerol dehydratase with 1,2-propanediol bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R9Epdb entry 1R9E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION6.5PEG 3350, TRI-AMMONIUM CITRATE, CAPILLARY BATCH, pH 6.5, EVAPORATION
Crystal Properties
Matthews coefficientSolvent content
3.0759.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.696α = 90
b = 212.399β = 90
c = 198.74γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayIMAGE PLATERIGAKU RAXIS IV2003-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.45097.7867248328322

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTpdb entry 1R9E2.446.2281.338328383145416297.870.17240.17010.2149random
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_d14.292
f_angle_d1.065
f_chiral_restr0.074
f_bond_d0.008
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12380
Nucleic Acid Atoms
Solvent Atoms896
Heterogen Atoms10

Software

Software
Software NamePurpose
PHENIXrefinement