5ZZK

A Con Artist: Phenylphenoxybenzamide is not a Glycosyltransferase Inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VMQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8278.15100 mM MgCl2, 100 mM Na HEPES pH 8, and 16 % wt/vol PEG400 (Sigma)
Crystal Properties
Matthews coefficientSolvent content
363.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.88α = 90
b = 39.64β = 90
c = 55.83γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDRAYONIX MX300HE2015-08-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A10.97622NSRRCBL15A1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.6430519.12.18774
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)
12.642.71510.443.52.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3VMQ2.6430828146582.550.24930.24510.3273RANDOM39.947
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]
-1.992.3-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.314
r_dihedral_angle_3_deg21.154
r_dihedral_angle_4_deg9.46
r_dihedral_angle_1_deg6.872
r_angle_refined_deg2.142
r_angle_other_deg1.238
r_chiral_restr0.13
r_bond_refined_d0.021
r_gen_planes_refined0.008
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.314
r_dihedral_angle_3_deg21.154
r_dihedral_angle_4_deg9.46
r_dihedral_angle_1_deg6.872
r_angle_refined_deg2.142
r_angle_other_deg1.238
r_chiral_restr0.13
r_bond_refined_d0.021
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1497
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing