7Q32

Mutant D24G of uridine phosphorylase from E. coli


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
1.8834.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.07α = 90
b = 150.07β = 90
c = 46.36γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.9537ESRFMASSIF-1

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
11.683010019.97.344388
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)
11.681.720.58

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-VALUE4R2X1.73042872215599.9670.1560.1540.202128.629
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]
-0.124-0.062-0.1240.403
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.33
r_dihedral_angle_4_deg23.276
r_dihedral_angle_3_deg14.566
r_dihedral_angle_1_deg7.151
r_lrange_it5.946
r_scangle_it5.707
r_scbond_it4.29
r_mcangle_it2.876
r_mcbond_it2.352
r_angle_refined_deg2.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.33
r_dihedral_angle_4_deg23.276
r_dihedral_angle_3_deg14.566
r_dihedral_angle_1_deg7.151
r_lrange_it5.946
r_scangle_it5.707
r_scbond_it4.29
r_mcangle_it2.876
r_mcbond_it2.352
r_angle_refined_deg2.103
r_nbtor_refined0.308
r_nbd_refined0.217
r_symmetry_nbd_refined0.207
r_xyhbond_nbd_refined0.146
r_chiral_restr0.137
r_symmetry_xyhbond_nbd_refined0.123
r_metal_ion_refined0.115
r_bond_refined_d0.014
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3752
Nucleic Acid Atoms
Solvent Atoms332
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing