5EPU

X-ray structure uridine phosphorylase from Vibrio cholerae in complex with cytosine at 1.06A.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4K6O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293PEG4000, 0.1M TRIS-HCl, 0.2M MgCl2x6H2O
Crystal Properties
Matthews coefficientSolvent content
2.2244.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.848α = 90
b = 96.715β = 119.96
c = 92.89γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2015-05-16MMAD
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)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
11.0646.46195.60.06616.266.5615831-311.28
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)
11.061.1283.70.6082.54

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 REPLACEMENTTHROUGHOUT4K6O1.0646.465853433049095.70.1060.1050.122RANDOM11.75
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]
-0.39-0.260.94-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free33.454
r_dihedral_angle_2_deg29.286
r_dihedral_angle_4_deg18.518
r_dihedral_angle_3_deg12.223
r_sphericity_bonded9.785
r_dihedral_angle_1_deg6.005
r_rigid_bond_restr3.736
r_mcangle_it1.633
r_angle_refined_deg1.504
r_mcbond_it1.229
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free33.454
r_dihedral_angle_2_deg29.286
r_dihedral_angle_4_deg18.518
r_dihedral_angle_3_deg12.223
r_sphericity_bonded9.785
r_dihedral_angle_1_deg6.005
r_rigid_bond_restr3.736
r_mcangle_it1.633
r_angle_refined_deg1.504
r_mcbond_it1.229
r_mcbond_other1.228
r_angle_other_deg0.974
r_chiral_restr0.092
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
MAIN-CHAIN ANGLE OTHER ATOMS (A**2)
r_scbond_it
SIDE-CHAIN BOND OTHER ATOMS (A**2)
r_scangle_it
SIDE-CHAIN ANGLE OTHER ATOMS (A**2)
LONG RANGE B REFINED ATOMS (A**2)
LONG RANGE B OTHER ATOMS (A**2)
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11299
Nucleic Acid Atoms
Solvent Atoms2207
Heterogen Atoms306

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing