8I69

Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with 5-Fluoroorotic 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
2.0339.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.11α = 90
b = 64.14β = 112.48
c = 45.28γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2020-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
1223.9995.310.0850.9917.63213394
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)
122.0720.4110.61

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 REPLACEMENTTHROUGHOUT4WS4223.991273665995.320.17670.174290.22482RANDOM22.032
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]
-0.380.30.35-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.171
r_dihedral_angle_4_deg20.637
r_dihedral_angle_3_deg13.173
r_dihedral_angle_1_deg6.474
r_long_range_B_refined4.818
r_long_range_B_other4.737
r_scangle_other2.708
r_angle_other_deg2.277
r_mcangle_it2.186
r_mcangle_other2.185
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.171
r_dihedral_angle_4_deg20.637
r_dihedral_angle_3_deg13.173
r_dihedral_angle_1_deg6.474
r_long_range_B_refined4.818
r_long_range_B_other4.737
r_scangle_other2.708
r_angle_other_deg2.277
r_mcangle_it2.186
r_mcangle_other2.185
r_scbond_it1.619
r_scbond_other1.618
r_angle_refined_deg1.361
r_mcbond_it1.311
r_mcbond_other1.306
r_chiral_restr0.062
r_bond_other_d0.035
r_gen_planes_other0.007
r_bond_refined_d0.005
r_gen_planes_refined0.005
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 Atoms192
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing