4WS8

Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with 2-thiouracil, Form V


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3A7N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH5.6293Ammonium acetate, Sodium citrate tribasic dihydrate, PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.0540.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.06α = 90
b = 45.07β = 90
c = 122.06γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.978565ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.440.691000.1039.3641291
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.481000.9231.96

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 REPLACEMENTTHROUGHOUT3A7N1.440.6939146207299.990.133760.1320.16757RANDOM16.46
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]
0.91-0.49-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.317
r_sphericity_free34.478
r_dihedral_angle_4_deg19.626
r_dihedral_angle_3_deg12.286
r_sphericity_bonded9.801
r_dihedral_angle_1_deg5.64
r_long_range_B_refined4.697
r_long_range_B_other4.121
r_scangle_other3.939
r_scbond_it3.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.317
r_sphericity_free34.478
r_dihedral_angle_4_deg19.626
r_dihedral_angle_3_deg12.286
r_sphericity_bonded9.801
r_dihedral_angle_1_deg5.64
r_long_range_B_refined4.697
r_long_range_B_other4.121
r_scangle_other3.939
r_scbond_it3.63
r_scbond_other3.629
r_rigid_bond_restr2.472
r_mcangle_it2.294
r_mcangle_other2.293
r_mcbond_it1.776
r_mcbond_other1.763
r_angle_refined_deg1.631
r_angle_other_deg0.877
r_chiral_restr0.094
r_bond_refined_d0.012
r_bond_other_d0.001
r_gen_planes_refined0.001
r_gen_planes_other
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1750
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing