8I6D

Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with 5-Hydroxy-2,4(1H,3H)-pyrimidinedione, Form VI


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WS4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH2930.1 M Tris pH 6.5, 1.4 M Sodium citrate, 15% PEG (w/v) 3350, 2% Benzamidine hydrochloride
Crystal Properties
Matthews coefficientSolvent content
2.0239.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.98α = 90
b = 77.99β = 102.02
c = 59.37γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2020-08-20MSINGLE 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
12.425.6196.280.12490.9735.55215539
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)
12.42.4860.3910.667

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 REPLACEMENTTHROUGHOUT4WS42.425.611478475596.290.20320.199860.26973RANDOM17.162
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]
0.89-0.91-1.210.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.584
r_dihedral_angle_4_deg16.025
r_dihedral_angle_3_deg15.698
r_dihedral_angle_1_deg7.336
r_long_range_B_refined3.516
r_long_range_B_other3.509
r_mcangle_it1.675
r_mcangle_other1.675
r_scangle_other1.503
r_angle_refined_deg1.476
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.584
r_dihedral_angle_4_deg16.025
r_dihedral_angle_3_deg15.698
r_dihedral_angle_1_deg7.336
r_long_range_B_refined3.516
r_long_range_B_other3.509
r_mcangle_it1.675
r_mcangle_other1.675
r_scangle_other1.503
r_angle_refined_deg1.476
r_angle_other_deg1.184
r_mcbond_it0.96
r_mcbond_other0.96
r_scbond_it0.855
r_scbond_other0.855
r_chiral_restr0.062
r_bond_refined_d0.006
r_gen_planes_refined0.005
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 Atoms3342
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing