5LBX

Structure of the T175V Etr1p mutant in the trigonal form P312 in complex with NADP and crotonyl-CoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4W99 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.4298Etr1p was crystallized at 15 mg/mL with 5 mM NADP and 5 mM of crotonyl-CoA in the gel filtration buffer (100 mM NaCl, 20 mM Tris-HCl pH 7.9). Crystals appeared after several days in 2.0 M (NH4)2SO4, 100 mM ADA/NaOH pH 6.4 at room temperature. The crystals were soaked in a solution containing 30% (v/v) glycerol, 2.0 M (NH4)2SO4, 100 mM ADA pH 6.4 prior to freezing in liquid nitrogen to prevent water-crystal formation.
Crystal Properties
Matthews coefficientSolvent content
3.4764.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.498α = 90
b = 93.498β = 90
c = 231.203γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.73913SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)CC (Half)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
12.547.041000.1240.0440.99712.28.641476
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)
12.52.641001.5111.57.7

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4W992.546.7491.3341370195899.840.18350.1820.2124
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_d15.216
f_angle_d1.002
f_chiral_restr0.054
f_bond_d0.007
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5596
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms224

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing