4WPL

Crystal structure of Mycobacterium tuberculosis uracil-DNA glycosylase in complex with uracil, Form I


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH4.6293Ammonium acetate, sodium acetate trihydrate, PEG 4000, hexafluoro 2-propanol
Crystal Properties
Matthews coefficientSolvent content
2.1141.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.91α = 90
b = 63.9β = 112.23
c = 45.08γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2012-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.95372ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.1519.839812.2370859
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.151.21903.62.5

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 REPLACEMENTTHROUGHOUT3A7N1.1519.8367265356897.890.104770.103760.12354RANDOM11.387
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]
-0.28-0.040.67-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.124
r_sphericity_free33.857
r_dihedral_angle_4_deg17.285
r_dihedral_angle_3_deg11.546
r_sphericity_bonded7.574
r_dihedral_angle_1_deg5.686
r_rigid_bond_restr4.981
r_long_range_B_refined3.702
r_long_range_B_other2.957
r_scangle_other2.765
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.124
r_sphericity_free33.857
r_dihedral_angle_4_deg17.285
r_dihedral_angle_3_deg11.546
r_sphericity_bonded7.574
r_dihedral_angle_1_deg5.686
r_rigid_bond_restr4.981
r_long_range_B_refined3.702
r_long_range_B_other2.957
r_scangle_other2.765
r_scbond_it2.328
r_scbond_other2.328
r_angle_refined_deg1.881
r_mcangle_it1.464
r_mcangle_other1.464
r_mcbond_it1.211
r_mcbond_other1.209
r_angle_other_deg0.927
r_chiral_restr0.126
r_bond_refined_d0.018
r_gen_planes_refined0.01
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 Atoms1733
Nucleic Acid Atoms
Solvent Atoms241
Heterogen Atoms55

Software

Software
Software NamePurpose
iMOSFLMdata processing
SCALAdata scaling
REFMACrefinement