5EFO

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytidine and cytosine at 1.63A.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293PEG4000, 0.1M TRIS-HCl, 0.2M MgCl2x6H2O
Crystal Properties
Matthews coefficientSolvent content
2.2445.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.949α = 67.54
b = 76.336β = 73.74
c = 89.694γ = 84.92
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2015-05-15MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.97989BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.6345.15793.20.080.0960.05310.53.3164109164109
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.631.7284.20.4280.4280.2811.73.221679

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 REPLACEMENTTHROUGHOUT4LWZ1.6319.97154258801192.160.16520.1630.2073RANDOM20.75
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]
-0.16-0.170.04-0.07-0.110.13
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.684
r_dihedral_angle_2_deg29.252
r_sphericity_bonded19.343
r_dihedral_angle_4_deg18.176
r_dihedral_angle_3_deg13.038
r_dihedral_angle_1_deg5.427
r_mcangle_it3.311
r_rigid_bond_restr3.09
r_scbond_it3.069
r_mcbond_it2.515
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.684
r_dihedral_angle_2_deg29.252
r_sphericity_bonded19.343
r_dihedral_angle_4_deg18.176
r_dihedral_angle_3_deg13.038
r_dihedral_angle_1_deg5.427
r_mcangle_it3.311
r_rigid_bond_restr3.09
r_scbond_it3.069
r_mcbond_it2.515
r_angle_refined_deg1.191
r_chiral_restr0.078
r_bond_refined_d0.007
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11262
Nucleic Acid Atoms
Solvent Atoms1518
Heterogen Atoms78

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction