7Q2W

Mutant T91S of uridine phosphorylase from Shewanella oneidensis


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M Bis-Tris, pH 6.5, 0.2 M ammonium sulfate, PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.244.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.4α = 90
b = 95.49β = 120.025
c = 91.41γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2016-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONKURCHATOV SNC BEAMLINE K4.40.964KURCHATOV 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
11.6525970.998.85.09159146
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)
11.651.750.88

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-VALUE4R2X1.65425159145778098.2890.1930.19090.232417.455
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]
-18.41-8.1432.512-14.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.876
r_dihedral_angle_4_deg18.049
r_dihedral_angle_3_deg15.799
r_dihedral_angle_1_deg8.696
r_lrange_it4.351
r_lrange_other4.351
r_scangle_it2.925
r_scangle_other2.923
r_mcangle_it2.916
r_mcangle_other2.916
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.876
r_dihedral_angle_4_deg18.049
r_dihedral_angle_3_deg15.799
r_dihedral_angle_1_deg8.696
r_lrange_it4.351
r_lrange_other4.351
r_scangle_it2.925
r_scangle_other2.923
r_mcangle_it2.916
r_mcangle_other2.916
r_angle_refined_deg2.315
r_scbond_it2.197
r_scbond_other2.194
r_mcbond_it2.179
r_mcbond_other2.178
r_angle_other_deg1.537
r_xyhbond_nbd_refined0.233
r_nbd_other0.228
r_symmetry_xyhbond_nbd_refined0.217
r_nbd_refined0.214
r_xyhbond_nbd_other0.212
r_symmetry_nbd_other0.201
r_nbtor_refined0.177
r_symmetry_nbd_refined0.151
r_chiral_restr0.116
r_symmetry_xyhbond_nbd_other0.109
r_symmetry_nbtor_other0.088
r_bond_refined_d0.018
r_gen_planes_refined0.015
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10898
Nucleic Acid Atoms
Solvent Atoms839
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing