8I63

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH6.52930.1 M Bis-Tris pH 6.5, 25% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.9837.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.38α = 90
b = 59.7β = 90
c = 73.65γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2020-08-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54179

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
11.9528.8497.90.0540.9968.01215145
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)
11.952.020.40250.678

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 REPLACEMENTTHROUGHOUT4WRV1.9528.861442671997.910.178090.175990.21886RANDOM29.181
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]
-0.67-0.651.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.433
r_dihedral_angle_4_deg20.121
r_dihedral_angle_3_deg14.039
r_long_range_B_refined7.17
r_long_range_B_other7.166
r_dihedral_angle_1_deg6.855
r_scangle_other4.649
r_mcangle_it3.507
r_mcangle_other3.506
r_scbond_it2.923
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.433
r_dihedral_angle_4_deg20.121
r_dihedral_angle_3_deg14.039
r_long_range_B_refined7.17
r_long_range_B_other7.166
r_dihedral_angle_1_deg6.855
r_scangle_other4.649
r_mcangle_it3.507
r_mcangle_other3.506
r_scbond_it2.923
r_scbond_other2.922
r_mcbond_it2.329
r_mcbond_other2.322
r_angle_refined_deg1.52
r_angle_other_deg1.296
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.007
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 Atoms1686
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing