1RXU

E. coli uridine phosphorylase: thymidine phosphate complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherA SINGLE HEXAMER (CHAINS ABCDEF) OF THE 5-FLUOROURACIL PHOSPHATE UP COMPLEX MODEL.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH METHOD UNDER OIL7.5289TRIS HCL, PEG4000, POTASSIUM ACETATE, THYMIDINE, POTASSIUM PHOSPHATE, pH 7.50, BATCH METHOD UNDER OIL, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.243.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 156.244α = 90
b = 97.655β = 118.23
c = 161.453γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray115IMAGE PLATEMARRESEARCHOSMIC2002-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
13.141.8998.20.1584.72.6764107641061.398
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)
13.13.26970.5291.42.55116

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTA SINGLE HEXAMER (CHAINS ABCDEF) OF THE 5-FLUOROURACIL PHOSPHATE UP COMPLEX MODEL.3.1257218172181382497.520.212560.212560.211670.22945RANDOM26.192
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]
-0.810.331.57-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.707
r_scangle_it4.054
r_scbond_it2.157
r_mcangle_it1.447
r_angle_refined_deg1.162
r_mcbond_it0.715
r_symmetry_vdw_refined0.648
r_symmetry_hbond_refined0.451
r_nbd_refined0.208
r_xyhbond_nbd_refined0.142
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.707
r_scangle_it4.054
r_scbond_it2.157
r_mcangle_it1.447
r_angle_refined_deg1.162
r_mcbond_it0.715
r_symmetry_vdw_refined0.648
r_symmetry_hbond_refined0.451
r_nbd_refined0.208
r_xyhbond_nbd_refined0.142
r_metal_ion_refined0.123
r_chiral_restr0.093
r_bond_refined_d0.01
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms33840
Nucleic Acid Atoms
Solvent Atoms1062
Heterogen Atoms405

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4data scaling