8I65

Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with isoorotic acid (2,4-Dihydroxypyrimidine-5-carboxylic 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
238.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.13α = 90
b = 63.22β = 112.93
c = 45.38γ = 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
11.7241.7997.40.0860.9824.92.320977
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)
11.721.820.1670.967

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 REPLACEMENTTHROUGHOUT4WS41.7234.8919842109897.130.192530.18940.25024RANDOM16.807
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]
1.080.10.57-1.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.899
r_dihedral_angle_4_deg18.324
r_dihedral_angle_3_deg14.28
r_dihedral_angle_1_deg6.529
r_long_range_B_refined4.975
r_long_range_B_other4.745
r_scangle_other2.514
r_mcangle_it1.687
r_mcangle_other1.686
r_scbond_it1.609
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.899
r_dihedral_angle_4_deg18.324
r_dihedral_angle_3_deg14.28
r_dihedral_angle_1_deg6.529
r_long_range_B_refined4.975
r_long_range_B_other4.745
r_scangle_other2.514
r_mcangle_it1.687
r_mcangle_other1.686
r_scbond_it1.609
r_scbond_other1.609
r_angle_refined_deg1.524
r_angle_other_deg1.314
r_mcbond_it1.08
r_mcbond_other1.074
r_chiral_restr0.074
r_gen_planes_refined0.008
r_bond_refined_d0.007
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 Atoms1739
Nucleic Acid Atoms
Solvent Atoms297
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing