8I6B

Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with 5-Hydroxy-2,4(1H,3H)-pyrimidinedione, 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 Tris pH 5.5, 25% PEG (w/v) 3350
Crystal Properties
Matthews coefficientSolvent content
2.0238.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.16α = 90
b = 63.68β = 112.58
c = 45.19γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2021-07-06MSINGLE 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
11.630.4993.720.03680.99511.77225418
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)
11.61.6570.14430.927

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 REPLACEMENTTHROUGHOUT4WS41.630.4924223119693.730.150570.149020.1816RANDOM11.572
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]
0.20.140.17-0.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.186
r_dihedral_angle_4_deg20.297
r_dihedral_angle_3_deg12.902
r_dihedral_angle_1_deg6.335
r_long_range_B_refined4.642
r_long_range_B_other4.393
r_scangle_other2.7
r_angle_other_deg2.308
r_scbond_it1.786
r_scbond_other1.785
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.186
r_dihedral_angle_4_deg20.297
r_dihedral_angle_3_deg12.902
r_dihedral_angle_1_deg6.335
r_long_range_B_refined4.642
r_long_range_B_other4.393
r_scangle_other2.7
r_angle_other_deg2.308
r_scbond_it1.786
r_scbond_other1.785
r_angle_refined_deg1.781
r_mcangle_it1.559
r_mcangle_other1.559
r_mcbond_it1.003
r_mcbond_other0.995
r_chiral_restr0.093
r_bond_other_d0.034
r_gen_planes_other0.019
r_bond_refined_d0.013
r_gen_planes_refined0.011
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 Atoms1739
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing