3FWP

X-ray structure of uridine nucleoside phosphorylease from Salmonella typhimurium complexed with phosphate and its inhibitor 2,2'-anhydrouridine at 1.86 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.2295PEG400, NaN3, GLYCEROL, PEG3350. K2HPO4, ANU, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2745.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.79α = 90
b = 124.07β = 90
c = 134.1γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2004-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.85EMBL/DESY, HAMBURGX13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.868888.40.094124633110180-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.861.8793.60.5062.491963

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 REPLACEMENTTHROUGHOUT3DPS1.8627.99104669550988.440.177650.176150.20617RANDOM20.376
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]
0.8-0.3-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.064
r_dihedral_angle_4_deg15.724
r_dihedral_angle_3_deg12.966
r_dihedral_angle_1_deg5.596
r_scangle_it1.922
r_scbond_it1.072
r_angle_refined_deg1.066
r_mcangle_it0.819
r_mcbond_it0.436
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.064
r_dihedral_angle_4_deg15.724
r_dihedral_angle_3_deg12.966
r_dihedral_angle_1_deg5.596
r_scangle_it1.922
r_scbond_it1.072
r_angle_refined_deg1.066
r_mcangle_it0.819
r_mcbond_it0.436
r_nbtor_refined0.294
r_nbd_refined0.19
r_symmetry_vdw_refined0.145
r_symmetry_hbond_refined0.112
r_xyhbond_nbd_refined0.109
r_metal_ion_refined0.099
r_chiral_restr0.069
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10965
Nucleic Acid Atoms
Solvent Atoms1015
Heterogen Atoms66

Software

Software
Software NamePurpose
DENZOdata reduction
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling