8I66

Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with isoorotic acid (2,4-Dihydroxypyrimidine-5-carboxylic 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
1MICROBATCH8.52930.1 M Bis-Tris pH 5.5, 0.5 M Sodium citrate, 25% PEG (w/v) 3350
Crystal Properties
Matthews coefficientSolvent content
2.0439.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.12α = 90
b = 63.97β = 112.29
c = 45.39γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2020-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU ULTRAX 181.54179

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
12.64297.60.1760.9766.13.76291
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)
12.62.740.6530.647

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 REPLACEMENTTHROUGHOUT4WS42.636.22595632497.260.181380.17820.23415RANDOM33.867
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]
0.221.22-0.58-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.535
r_dihedral_angle_4_deg23.643
r_dihedral_angle_3_deg17.382
r_dihedral_angle_1_deg7.048
r_long_range_B_refined5.924
r_long_range_B_other5.923
r_mcangle_it3.824
r_mcangle_other3.822
r_scangle_other3.679
r_mcbond_it2.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.535
r_dihedral_angle_4_deg23.643
r_dihedral_angle_3_deg17.382
r_dihedral_angle_1_deg7.048
r_long_range_B_refined5.924
r_long_range_B_other5.923
r_mcangle_it3.824
r_mcangle_other3.822
r_scangle_other3.679
r_mcbond_it2.34
r_mcbond_other2.34
r_scbond_it2.312
r_scbond_other2.28
r_angle_refined_deg1.496
r_angle_other_deg1.174
r_chiral_restr0.055
r_bond_refined_d0.007
r_gen_planes_refined0.006
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 Atoms1728
Nucleic Acid Atoms
Solvent Atoms36
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing