3EUF

Crystal structure of BAU-bound human uridine phosphorylase 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U1CPDB ENTRY 1U1C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529817% PEG 3350, 300mM KCl, 30mM MgCl2, 100mM Bis-Tris Buffer, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2445.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.197α = 90
b = 74.442β = 90
c = 262.707γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.00000SSRLBL7-1

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
11.95099.80.11916.110.6103357103213
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)
1.91.971001000.441210192

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1U1C1.95097957515599.760.204810.20240.25147RANDOM29.999
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]
0.790.81-1.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.707
r_dihedral_angle_4_deg19.244
r_dihedral_angle_3_deg14.157
r_dihedral_angle_1_deg5.972
r_scangle_it4.524
r_scbond_it3.024
r_mcangle_it1.91
r_angle_refined_deg1.721
r_mcbond_it1.268
r_symmetry_hbond_refined0.412
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.707
r_dihedral_angle_4_deg19.244
r_dihedral_angle_3_deg14.157
r_dihedral_angle_1_deg5.972
r_scangle_it4.524
r_scbond_it3.024
r_mcangle_it1.91
r_angle_refined_deg1.721
r_mcbond_it1.268
r_symmetry_hbond_refined0.412
r_nbtor_refined0.303
r_symmetry_vdw_refined0.234
r_nbd_refined0.204
r_xyhbond_nbd_refined0.164
r_chiral_restr0.112
r_bond_refined_d0.018
r_gen_planes_refined0.008
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 Atoms9030
Nucleic Acid Atoms
Solvent Atoms336
Heterogen Atoms100

Software

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