4K6O

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with 6-methyluracil at 1.17 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4IP0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5286PEG4000, 0.1M TRIS-HCl, 0.2M MgCl2x6H2O, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Crystal Properties
Matthews coefficientSolvent content
2.2445.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.012α = 90
b = 97.1β = 119.99
c = 93.017γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.826PETRA III, EMBL c/o DESYP13 (MX1)

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
11.1780.5690.70.03811.95449315-312.83
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)
11.171.255.30.2043.23

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT4IP01.1740.281.364779504492732253694.10.110.1080.12813.2
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_d12.046
f_angle_d1.185
f_chiral_restr0.067
f_bond_d0.016
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11243
Nucleic Acid Atoms
Solvent Atoms2482
Heterogen Atoms161

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction