4WGF

YcaC from Pseudomonas aeruginosa with hexane-2,5-diol and covalent acrylamide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.75292Crystal produced from streak seeding. Mother liquor: 26% w/v PEG 3350, 400 mM (NH4)2SO4, and 70 mM BisTris-HCl pH 6.75. Protein buffer: 50 mM NaCl, 50 mM Tris-HCl pH 7.4, 4% 1-,4-dioxane, and 0.1 mM TCEP.
Crystal Properties
Matthews coefficientSolvent content
2.3447.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 158.36α = 90
b = 74.48β = 92.29
c = 141.06γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.9537SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.3431.72870.155911.6846039012.18
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.342.424360.2764.591.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1YAC2.3402069084831.721.3359200658160346305886.80254887010.1737998207150.1721828214470.203845887682Random selection14.9697430435
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_d11.1788438853
f_angle_d0.670963407373
f_chiral_restr0.0278780703328
f_plane_restr0.00266053029077
f_bond_d0.0023316997053
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12488
Nucleic Acid Atoms
Solvent Atoms1059
Heterogen Atoms157

Software

Software
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling
PHASERphasing