4WS1

Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with 5-fluorouracil (AB), Form II


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH8.5293Sodim acetate trihydrate, Tris hydrochloride, PEG 4000, 1,3-butanediol
Crystal Properties
Matthews coefficientSolvent content
1.9737.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.71α = 90
b = 43.64β = 99.1
c = 67.6γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.976254ESRFBM14

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
11.436.8698.30.115117.139017
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)
11.41.4888.90.6862.25.1

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 REPLACEMENTTHROUGHOUT3A7N1.436.8637056196198.320.134830.132590.17552RANDOM11.758
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]
0.54-0.2-0.3-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.741
r_dihedral_angle_2_deg34.984
r_dihedral_angle_4_deg15.741
r_dihedral_angle_3_deg11.264
r_sphericity_bonded8.165
r_dihedral_angle_1_deg6.112
r_long_range_B_refined4.17
r_rigid_bond_restr3.924
r_long_range_B_other3.319
r_scangle_other3.14
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.741
r_dihedral_angle_2_deg34.984
r_dihedral_angle_4_deg15.741
r_dihedral_angle_3_deg11.264
r_sphericity_bonded8.165
r_dihedral_angle_1_deg6.112
r_long_range_B_refined4.17
r_rigid_bond_restr3.924
r_long_range_B_other3.319
r_scangle_other3.14
r_scbond_it2.757
r_scbond_other2.753
r_mcangle_other2.078
r_mcangle_it2.075
r_angle_refined_deg1.907
r_mcbond_it1.722
r_mcbond_other1.718
r_angle_other_deg0.991
r_chiral_restr0.137
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_gen_planes_other0.002
r_bond_other_d0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1692
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing