2R0T

Crystal structure of GDP-4-keto-6-deoxymannose-3-dehydratase with a trapped PLP-glutamate geminal diamine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GMUPDB entry 2GMU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1629824% PEG 3400, 100mM MES, 600mM KCl, 2mM PLP, 2mM 2-oxoglutarate, pH 6.0, batch, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3848.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.908α = 90
b = 72.905β = 107.94
c = 86.959γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDBRUKER PROTEUMmontel opics2007-06-20SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
11.93092.80.06269.872.917710560929
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9283.30.41.551.427757

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2GMU1.93065664609236003930.1850.1850.1830.255random40.852
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6184
Nucleic Acid Atoms
Solvent Atoms258
Heterogen Atoms50

Software

Software
Software NamePurpose
EPMRphasing
TNTrefinement
PDB_EXTRACTdata extraction
cosmodata collection
SAINTdata reduction
SADABSdata scaling