2HRD

Crystal structure of the uridine phosphorylase from Salmonella typhimurium in complex with thymine and phosphate ion at 1.70A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZL2PDB ENTRY 1ZL2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
129725% PEG 400, 0.1M potassium phosphate, 0.2M magnesium chloride, 0.1M cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.2244.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.2α = 90
b = 123.4β = 90
c = 133.2γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRRORS2005-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/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
11.730159741
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.74

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 1ZL21.730151618798099.940.167420.16630.18883RANDOM8.391
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]
-0.040.2-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.43
r_dihedral_angle_4_deg15.326
r_dihedral_angle_3_deg13.033
r_dihedral_angle_1_deg5.558
r_sphericity_free1.695
r_scangle_it1.611
r_angle_refined_deg1.067
r_scbond_it0.972
r_sphericity_bonded0.828
r_mcangle_it0.826
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.43
r_dihedral_angle_4_deg15.326
r_dihedral_angle_3_deg13.033
r_dihedral_angle_1_deg5.558
r_sphericity_free1.695
r_scangle_it1.611
r_angle_refined_deg1.067
r_scbond_it0.972
r_sphericity_bonded0.828
r_mcangle_it0.826
r_rigid_bond_restr0.592
r_mcbond_it0.491
r_nbtor_refined0.299
r_nbd_refined0.192
r_symmetry_vdw_refined0.189
r_xyhbond_nbd_refined0.099
r_symmetry_hbond_refined0.098
r_chiral_restr0.071
r_bond_refined_d0.006
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11116
Nucleic Acid Atoms
Solvent Atoms705
Heterogen Atoms140

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing