3KVV

Trapping of an oxocarbenium ion intermediate in UP crystals


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.32955% PEG4K, 5% glycerol, 100 mM MES, pH 6.3, vapor diffusion, hanging drop, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2144.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.864α = 90
b = 92.864β = 90
c = 145.016γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 8-BMAPS8-BM

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
11.850123229
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.8

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (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 REPLACEMENT1.823.520.03120598599293.50.1750.1730.20525.49
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]
-0.767-1.215-0.7671.533
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.916
f_angle_d1.174
f_chiral_restr0.072
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10861
Nucleic Acid Atoms
Solvent Atoms698
Heterogen Atoms138

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
CNSrefinement