8I6A

Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with Orotic 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% PEG (w/v) 3350
Crystal Properties
Matthews coefficientSolvent content
2.0239.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.58α = 90
b = 59.7β = 90
c = 75.07γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2020-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU ULTRAX 181.5418

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
1246.7396.440.0330.99513.57214172
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)
122.0720.1690.903

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 REPLACEMENTTHROUGHOUT4WRV246.731351066296.450.169970.167570.22079RANDOM20.472
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]
-0.63-0.661.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.134
r_dihedral_angle_4_deg21.051
r_dihedral_angle_3_deg12.297
r_dihedral_angle_1_deg6.678
r_long_range_B_refined5.922
r_long_range_B_other5.852
r_scangle_other3.629
r_mcangle_it2.766
r_mcangle_other2.765
r_scbond_it2.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.134
r_dihedral_angle_4_deg21.051
r_dihedral_angle_3_deg12.297
r_dihedral_angle_1_deg6.678
r_long_range_B_refined5.922
r_long_range_B_other5.852
r_scangle_other3.629
r_mcangle_it2.766
r_mcangle_other2.765
r_scbond_it2.33
r_scbond_other2.328
r_angle_other_deg2.296
r_mcbond_it1.832
r_mcbond_other1.826
r_angle_refined_deg1.599
r_chiral_restr0.075
r_bond_other_d0.035
r_gen_planes_other0.013
r_bond_refined_d0.01
r_gen_planes_refined0.008
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 Atoms1691
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing