1RXS

E. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherDETWINNED HEXAMERIC NATIVE UP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH METHOD UNDER OIL7.5289TRIS HCL, PEG4000, POTASSIUM ACETATE, 2'-DEOXYURIDINE, SODIUM ORTHOVANADATE, pH 7.50, BATCH METHOD UNDER OIL, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2544.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.958α = 90
b = 98.212β = 109.09
c = 242.729γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray115IMAGE PLATEMARRESEARCHOSMIC2002-08-05MSINGLE 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
12.840.4997.80.1235.43.117352517352546.18
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)
12.82.9495.30.4131.83.119170

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 REPLACEMENTTHROUGHOUTDETWINNED HEXAMERIC NATIVE UP2.826.75166227166227872599.160.177940.177940.175850.21814RANDOM17.286
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]
-0.110.10.91-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.995
r_scangle_it3.011
r_scbond_it1.639
r_angle_refined_deg1.362
r_mcangle_it0.966
r_symmetry_vdw_refined0.552
r_symmetry_hbond_refined0.521
r_mcbond_it0.474
r_nbd_refined0.215
r_xyhbond_nbd_refined0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.995
r_scangle_it3.011
r_scbond_it1.639
r_angle_refined_deg1.362
r_mcangle_it0.966
r_symmetry_vdw_refined0.552
r_symmetry_hbond_refined0.521
r_mcbond_it0.474
r_nbd_refined0.215
r_xyhbond_nbd_refined0.15
r_chiral_restr0.088
r_metal_ion_refined0.071
r_bond_refined_d0.013
r_gen_planes_refined0.004
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 Atoms55267
Nucleic Acid Atoms
Solvent Atoms1581
Heterogen Atoms760

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4data scaling