8I61

Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with Barbituric acid and Citric acid, Form I


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH5.52930.1 M Bis-Tris pH 5.5, 0.5 M Sodium citrate, 25% PEG (w/v) 3350
Crystal Properties
Matthews coefficientSolvent content
2.0138.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.05α = 90
b = 63.65β = 112.82
c = 45.31γ = 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)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
11.2425.3193.90.9978.33.554220
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.241.310.681

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 REPLACEMENTTHROUGHOUT4WS41.2423.8551603257793.640.123230.121280.16304RANDOM13.582
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]
-0.020.24-0.210.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.895
r_dihedral_angle_4_deg20.893
r_dihedral_angle_3_deg13.58
r_dihedral_angle_1_deg6.297
r_rigid_bond_restr3.501
r_long_range_B_refined3.405
r_scangle_other2.921
r_long_range_B_other2.85
r_scbond_it2.688
r_scbond_other2.687
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.895
r_dihedral_angle_4_deg20.893
r_dihedral_angle_3_deg13.58
r_dihedral_angle_1_deg6.297
r_rigid_bond_restr3.501
r_long_range_B_refined3.405
r_scangle_other2.921
r_long_range_B_other2.85
r_scbond_it2.688
r_scbond_other2.687
r_angle_refined_deg2.059
r_mcangle_it1.809
r_mcangle_other1.809
r_angle_other_deg1.645
r_mcbond_it1.52
r_mcbond_other1.504
r_chiral_restr0.133
r_bond_refined_d0.017
r_gen_planes_refined0.013
r_bond_other_d0.002
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 Atoms1736
Nucleic Acid Atoms
Solvent Atoms327
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing