4WS5

Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with 5-nitrouracil, Form III


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3A7N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH6.5293Sodium acetate trihydrate, Sodium cacodylate trihydrate, PEG 8000, Jeffamine M-600
Crystal Properties
Matthews coefficientSolvent content
2.0239.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.52α = 90
b = 60.02β = 90
c = 74.88γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97625ESRFBM14

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
11.439.5299.60.06720.310.641836
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)
11.41.4897.20.4793.87

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 REPLACEMENTTHROUGHOUT3A7N1.439.5239662211499.450.122140.120130.16033RANDOM18.413
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]
-0.820.060.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.881
r_sphericity_free28.703
r_dihedral_angle_4_deg19.942
r_sphericity_bonded12.945
r_dihedral_angle_3_deg11.171
r_dihedral_angle_1_deg6.061
r_long_range_B_refined5.415
r_rigid_bond_restr4.922
r_long_range_B_other4.853
r_scangle_other4.751
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.881
r_sphericity_free28.703
r_dihedral_angle_4_deg19.942
r_sphericity_bonded12.945
r_dihedral_angle_3_deg11.171
r_dihedral_angle_1_deg6.061
r_long_range_B_refined5.415
r_rigid_bond_restr4.922
r_long_range_B_other4.853
r_scangle_other4.751
r_mcangle_it4.006
r_mcangle_other4.006
r_scbond_it3.886
r_scbond_other3.878
r_mcbond_it3.36
r_mcbond_other3.357
r_angle_refined_deg1.997
r_angle_other_deg0.971
r_chiral_restr0.124
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1691
Nucleic Acid Atoms
Solvent Atoms291
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing