7Q1I

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


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
1.8834.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.52α = 90
b = 150.52β = 90
c = 46.25γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2018-04-18MSINGLE 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
11.653097.917.92.2450485
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)
11.651.690.6

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-VALUE4R2X1.653046523235398.9470.1810.17880.229319.565
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]
0.2370.1180.237-0.768
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.811
r_dihedral_angle_4_deg22.782
r_dihedral_angle_3_deg14.63
r_dihedral_angle_1_deg7.372
r_lrange_it4.771
r_scangle_it4.41
r_scbond_it3.304
r_mcangle_it2.604
r_angle_refined_deg2.352
r_mcbond_it2.165
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.811
r_dihedral_angle_4_deg22.782
r_dihedral_angle_3_deg14.63
r_dihedral_angle_1_deg7.372
r_lrange_it4.771
r_scangle_it4.41
r_scbond_it3.304
r_mcangle_it2.604
r_angle_refined_deg2.352
r_mcbond_it2.165
r_nbtor_refined0.305
r_nbd_refined0.222
r_symmetry_nbd_refined0.18
r_chiral_restr0.147
r_symmetry_xyhbond_nbd_refined0.146
r_xyhbond_nbd_refined0.129
r_metal_ion_refined0.065
r_bond_refined_d0.018
r_gen_planes_refined0.016
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3766
Nucleic Acid Atoms
Solvent Atoms311
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing