1U1D

Structure of e. coli uridine phosphorylase complexed to 5-(phenylthio)acyclouridine (ptau)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2295PEG 4000, MES, GLYCEROL, PH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.4449.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.15α = 90
b = 125.746β = 90
c = 140.88γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152003-07-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 8-BM0.9790APS8-BM

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
1247.1499.97.3109591109591
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0799.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.00147.1495324953241064696.730.210980.210980.209250.22635RANDOM18.028
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]
-1.630.231.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.818
r_angle_refined_deg0.891
r_scangle_it0.614
r_scbond_it0.366
r_mcangle_it0.204
r_nbd_refined0.161
r_symmetry_hbond_refined0.122
r_symmetry_vdw_refined0.117
r_mcbond_it0.104
r_xyhbond_nbd_refined0.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg4.818
r_angle_refined_deg0.891
r_scangle_it0.614
r_scbond_it0.366
r_mcangle_it0.204
r_nbd_refined0.161
r_symmetry_hbond_refined0.122
r_symmetry_vdw_refined0.117
r_mcbond_it0.104
r_xyhbond_nbd_refined0.091
r_chiral_restr0.061
r_bond_refined_d0.005
r_gen_planes_refined0.002
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_refined
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 Atoms11273
Nucleic Acid Atoms
Solvent Atoms506
Heterogen Atoms153

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
MOSFLMdata reduction
CNSphasing