4R2X

Unique conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis uridine phosphorylase in the free form and in complex with uridine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RXY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.52930.75M ammonium sulfate, 0.1M Bis-Tris, pH 5.5, 0.75% (w/v) PEG 3350, 25% (v/v) glycerol, temperature 293K, FREE INTERFACE DIFFUSION, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.1643.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.54α = 90
b = 95.93β = 120
c = 91.61γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL24XUSPring-8BL24XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
10.9379.3593.50.1260.8712.25.38832881
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.95193.40.6610.7082.64.8

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 REPLACEMENTTHROUGHOUT1RXY0.9329.668348274336895.90.150.1490.164RANDOM8.86
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]
-2.61.6810.97-8.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.628
r_sphericity_free20.238
r_dihedral_angle_4_deg17.032
r_dihedral_angle_3_deg12.115
r_sphericity_bonded7.518
r_dihedral_angle_1_deg6.466
r_rigid_bond_restr4.586
r_long_range_B_refined2.049
r_long_range_B_other2.049
r_angle_refined_deg1.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.628
r_sphericity_free20.238
r_dihedral_angle_4_deg17.032
r_dihedral_angle_3_deg12.115
r_sphericity_bonded7.518
r_dihedral_angle_1_deg6.466
r_rigid_bond_restr4.586
r_long_range_B_refined2.049
r_long_range_B_other2.049
r_angle_refined_deg1.69
r_scangle_other1.64
r_scbond_it1.423
r_scbond_other1.423
r_mcangle_it1.248
r_mcangle_other1.248
r_mcbond_it0.988
r_mcbond_other0.988
r_angle_other_deg0.919
r_chiral_restr0.101
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10834
Nucleic Acid Atoms
Solvent Atoms1092
Heterogen Atoms158

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling