3C74

X-ray structure of the uridine phosphorylase from salmonella typhimurium in complex with 2,2'-anhydrouridine at 2.38a resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP297PEG400, NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.3547.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.37α = 90
b = 125.308β = 90
c = 135.177γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMAR CCD 165 mmmirrors2006-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X131.0500EMBL/DESY, HAMBURGX13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.382061088

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.3819.9459239184998.390.209440.207940.25787RANDOM34.733
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.5
r_dihedral_angle_4_deg15.996
r_dihedral_angle_3_deg14.026
r_dihedral_angle_1_deg5.026
r_angle_refined_deg1.154
r_scangle_it0.872
r_scbond_it0.529
r_mcangle_it0.498
r_nbtor_refined0.288
r_mcbond_it0.284
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.5
r_dihedral_angle_4_deg15.996
r_dihedral_angle_3_deg14.026
r_dihedral_angle_1_deg5.026
r_angle_refined_deg1.154
r_scangle_it0.872
r_scbond_it0.529
r_mcangle_it0.498
r_nbtor_refined0.288
r_mcbond_it0.284
r_nbd_refined0.166
r_symmetry_hbond_refined0.13
r_symmetry_vdw_refined0.129
r_xyhbond_nbd_refined0.104
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11005
Nucleic Acid Atoms
Solvent Atoms374
Heterogen Atoms96

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction