1R6D

Crystal Structure of DesIV double mutant (dTDP-glucose 4,6-dehydratase) from Streptomyces venezuelae with NAD and DAU bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R66 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Batch macro-seeding6.5277Peg 8000, magnesium chloride, cacodylate, pH 6.5, Batch macro-seeding, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.8131.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.7α = 90
b = 99.4β = 90
c = 42.2γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTORSIEMENS HI-STARGobel focusing optics2003-08-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.353091.90.0417.33.66166461664
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)
11.351.41810.22321.76573

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 REPLACEMENTTHROUGHOUT1R661.35306166461664618791.90.1760.1760.1740.216RANDOM
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
t_angle_deg2.35
t_bond_d0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2475
Nucleic Acid Atoms
Solvent Atoms371
Heterogen Atoms80

Software

Software
Software NamePurpose
FRAMBOdata collection
XSCALIBREdata reduction
AMoREphasing
TNTrefinement
XSCALIBREdata scaling