7Q1J

Hybrid form of uridine phosphorylase from E. coli and Salmonella typhimurium in the presence PEG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4R2X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.2 M Potassium citrate tribasic monohydrate, 20% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
1.8834.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.59α = 90
b = 150.59β = 90
c = 46.29γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2018-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONKURCHATOV SNC BEAMLINE K4.40.8025KURCHATOV SNCK4.4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.713099.519.63.8242058
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.711.750.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4R2X1.713042058214999.4510.2080.20370.280826.903
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]
0.710.3550.71-2.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.046
r_dihedral_angle_4_deg19.674
r_dihedral_angle_3_deg17.174
r_dihedral_angle_1_deg8.315
r_lrange_it6.773
r_scangle_it6.029
r_scbond_it4.752
r_mcangle_it4.667
r_mcbond_it3.893
r_angle_refined_deg2.609
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.046
r_dihedral_angle_4_deg19.674
r_dihedral_angle_3_deg17.174
r_dihedral_angle_1_deg8.315
r_lrange_it6.773
r_scangle_it6.029
r_scbond_it4.752
r_mcangle_it4.667
r_mcbond_it3.893
r_angle_refined_deg2.609
r_nbtor_refined0.315
r_metal_ion_refined0.234
r_nbd_refined0.232
r_symmetry_nbd_refined0.221
r_chiral_restr0.177
r_xyhbond_nbd_refined0.173
r_symmetry_xyhbond_nbd_refined0.165
r_gen_planes_refined0.019
r_bond_refined_d0.018
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3766
Nucleic Acid Atoms
Solvent Atoms283
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing