8I62

Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with Barbituric acid, 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
2.0339.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.28α = 90
b = 63.91β = 112.7
c = 45.28γ = 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
11.2636.2499.10.0430.998143.355586
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)
11.261.320.2210.948

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 REPLACEMENTTHROUGHOUT4WS41.2636.2652947261699.010.110590.108990.14319RANDOM17.861
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]
-0.160.82-0.37-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.798
r_dihedral_angle_4_deg19.708
r_dihedral_angle_3_deg11.985
r_rigid_bond_restr9.494
r_long_range_B_refined6.586
r_long_range_B_other6.276
r_dihedral_angle_1_deg6.155
r_scangle_other6.009
r_mcbond_it5.732
r_mcbond_other5.722
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.798
r_dihedral_angle_4_deg19.708
r_dihedral_angle_3_deg11.985
r_rigid_bond_restr9.494
r_long_range_B_refined6.586
r_long_range_B_other6.276
r_dihedral_angle_1_deg6.155
r_scangle_other6.009
r_mcbond_it5.732
r_mcbond_other5.722
r_mcangle_it5.495
r_mcangle_other5.493
r_scbond_it4.738
r_scbond_other4.736
r_angle_refined_deg2.022
r_angle_other_deg1.709
r_chiral_restr0.123
r_bond_refined_d0.02
r_bond_other_d0.014
r_gen_planes_refined0.012
r_gen_planes_other0.002
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1739
Nucleic Acid Atoms
Solvent Atoms367
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing