4EHT

Activator of the 2-Hydroxyisocaproyl-CoA dehydratase from Clostridium difficile with bound ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HUXPDB ENTRY 1HUX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.528925 mg/mL protein in 50 mM MOPS, pH 7.2, 0.3 M sodium chloride, 1 mM ADP, 10 mM magnesium chloride, 2.5 mM D-desthiobiotin, 2 mM DTT, 10 mM sodium dithionite, reservoir: 4 M ammonium acetate, 0.1 M Tris/HCl, pH 8.5 (drop: 2 uL + 2 uL), VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.6753.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.154α = 90
b = 161.005β = 110.75
c = 63.576γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252008-08-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

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
11.953099.40.0483.844923449232-3
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)
11.95299.70.5013.83282

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 1HUX1.9519.71.994492344923214599.610.17710.17560.2051RANDOM
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]
4.321311.0121-4.77050.4493
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.592
f_angle_d1.362
f_chiral_restr0.072
f_bond_d0.009
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3933
Nucleic Acid Atoms
Solvent Atoms271
Heterogen Atoms79

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling