8I68

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


X-RAY DIFFRACTION

Starting Model(s)

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

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
2.0138.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.37α = 90
b = 60.02β = 90
c = 74.47γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2021-04-22MSINGLE 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
11.8830.0191.350.04590.9858.82216264
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)
11.881.9470.3270.902

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 REPLACEMENTTHROUGHOUT4WRV1.8830.011518581291.370.210280.207510.26457RANDOM23.734
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]
-0.320.10.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.311
r_dihedral_angle_4_deg24.456
r_dihedral_angle_3_deg15.695
r_dihedral_angle_1_deg6.865
r_long_range_B_refined6.413
r_long_range_B_other6.393
r_scangle_other3.805
r_mcangle_other2.89
r_mcangle_it2.889
r_scbond_it2.377
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.311
r_dihedral_angle_4_deg24.456
r_dihedral_angle_3_deg15.695
r_dihedral_angle_1_deg6.865
r_long_range_B_refined6.413
r_long_range_B_other6.393
r_scangle_other3.805
r_mcangle_other2.89
r_mcangle_it2.889
r_scbond_it2.377
r_scbond_other2.376
r_mcbond_it1.908
r_mcbond_other1.903
r_angle_refined_deg1.536
r_angle_other_deg1.311
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.007
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1684
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing