8I67

Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with 2,4-Thiazolidinedione, Form I


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WS4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH8.52930.1 M Tris pH 8.5, 25% PEG (w/v) 3350
Crystal Properties
Matthews coefficientSolvent content
2.0239.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.28α = 90
b = 63.41β = 112.8
c = 45.44γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-08-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1.0ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.7234.95940.0860.996.72.920377
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.721.820.210.941

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 REPLACEMENTTHROUGHOUT4WS41.7234.9819162105292.920.18690.184150.24009RANDOM16.278
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]
0.440.370.7-1.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.324
r_dihedral_angle_4_deg20.699
r_dihedral_angle_3_deg14.045
r_dihedral_angle_1_deg6.417
r_long_range_B_refined4.341
r_long_range_B_other4.012
r_scangle_other2.341
r_mcangle_it1.612
r_mcangle_other1.612
r_scbond_it1.573
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.324
r_dihedral_angle_4_deg20.699
r_dihedral_angle_3_deg14.045
r_dihedral_angle_1_deg6.417
r_long_range_B_refined4.341
r_long_range_B_other4.012
r_scangle_other2.341
r_mcangle_it1.612
r_mcangle_other1.612
r_scbond_it1.573
r_scbond_other1.573
r_angle_refined_deg1.568
r_angle_other_deg1.361
r_mcbond_it1.081
r_mcbond_other1.078
r_chiral_restr0.082
r_gen_planes_refined0.009
r_bond_refined_d0.008
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 Atoms1734
Nucleic Acid Atoms
Solvent Atoms309
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing