4WS0

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH8.5293Sodium acetate trihydrate, Tris HCl, PEG 4000, 1,3-butanediol
Crystal Properties
Matthews coefficientSolvent content
1.9737.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.82α = 90
b = 43.67β = 99.11
c = 67.65γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2012-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54179

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
11.9736.8998.70.08910.33.414239
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)
11.972.0891.20.2314.93.2

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 REPLACEMENTTHROUGHOUT3A7N1.97436.891352371499.290.167550.164920.21805RANDOM13.051
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]
1.19-0.19-0.84-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.051
r_dihedral_angle_4_deg17.384
r_dihedral_angle_3_deg12.536
r_dihedral_angle_1_deg6.296
r_long_range_B_refined4.822
r_long_range_B_other4.44
r_scangle_other2.306
r_angle_refined_deg1.836
r_mcangle_other1.617
r_mcangle_it1.616
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.051
r_dihedral_angle_4_deg17.384
r_dihedral_angle_3_deg12.536
r_dihedral_angle_1_deg6.296
r_long_range_B_refined4.822
r_long_range_B_other4.44
r_scangle_other2.306
r_angle_refined_deg1.836
r_mcangle_other1.617
r_mcangle_it1.616
r_scbond_it1.424
r_scbond_other1.422
r_mcbond_it1.033
r_mcbond_other1.023
r_angle_other_deg0.944
r_chiral_restr0.108
r_bond_refined_d0.018
r_gen_planes_refined0.01
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 Atoms1698
Nucleic Acid Atoms
Solvent Atoms184
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing