3DMP

2.6 A crystal structure of uracil phosphoribosyltransferase from Burkholderia pseudomallei


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.52892M NaCl, 5% PEG 4000, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.9858.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.222α = 90
b = 80.637β = 99.11
c = 141.833γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDADJUSTABLE FOCUSING MIRRORS2008-04-04SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.00APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.55099.70.1554.13.739360
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.52.591000.7643.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.649.3333305175899.620.221450.218820.27053RANDOM45.41
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]
-0.040.020.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.853
r_dihedral_angle_3_deg20.261
r_dihedral_angle_4_deg19.764
r_dihedral_angle_1_deg6.713
r_scangle_it2.3
r_angle_refined_deg1.432
r_scbond_it1.363
r_mcangle_it1.027
r_mcbond_it0.581
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.853
r_dihedral_angle_3_deg20.261
r_dihedral_angle_4_deg19.764
r_dihedral_angle_1_deg6.713
r_scangle_it2.3
r_angle_refined_deg1.432
r_scbond_it1.363
r_mcangle_it1.027
r_mcbond_it0.581
r_nbtor_refined0.309
r_nbd_refined0.221
r_symmetry_hbond_refined0.215
r_symmetry_vdw_refined0.212
r_xyhbond_nbd_refined0.15
r_chiral_restr0.095
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_symmetry_vdw_other
r_nbd_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_angle_other_deg
r_mcbond_other
r_nbtor_other
r_gen_planes_other
r_bond_other_d
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6694
Nucleic Acid Atoms
Solvent Atoms83
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction