5XTK

Crystal structure of Xanthine-guanine phosphoribosyltransferase from Yersinia pestis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52980.2M Lithium sulphate, 25% PEG 3350, 0.1M HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.754.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.557α = 90
b = 66.557β = 90
c = 165.379γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.074NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.7466.5699.90.0670.0540.0690.0180.98710.614.43918115.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.741.7798.80.5840.4910.6140.1860.9233.7410.5

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 REPLACEMENTTHROUGHOUT1NUL1.7466.5637024193199.430.167730.166260.19654RANDOM20.616
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]
-0.2-0.20.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.039
r_dihedral_angle_4_deg20.956
r_dihedral_angle_3_deg13.421
r_dihedral_angle_1_deg6.495
r_long_range_B_refined4.16
r_long_range_B_other4.09
r_scangle_other2.817
r_mcangle_other2.141
r_mcangle_it2.139
r_angle_refined_deg1.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.039
r_dihedral_angle_4_deg20.956
r_dihedral_angle_3_deg13.421
r_dihedral_angle_1_deg6.495
r_long_range_B_refined4.16
r_long_range_B_other4.09
r_scangle_other2.817
r_mcangle_other2.141
r_mcangle_it2.139
r_angle_refined_deg1.84
r_scbond_it1.749
r_scbond_other1.749
r_mcbond_it1.294
r_mcbond_other1.267
r_angle_other_deg0.795
r_chiral_restr0.11
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2337
Nucleic Acid Atoms
Solvent Atoms178
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing