4WRV

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH6.5293Sodium acetate trihydrate, Sodium cacodylate trihydrate, PEG 8000, Jeffamine M-600
Crystal Properties
Matthews coefficientSolvent content
1.9837.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.45α = 90
b = 59.92β = 90
c = 73.36γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97372ESRFBM14

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
11.4432.831000.1110.87.237819
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)
11.441.521001.0343.17.2

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 REPLACEMENTTHROUGHOUT3A7N1.4432.8335869188699.920.122140.121160.1402RANDOM16.473
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]
-0.35-0.210.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.612
r_sphericity_free35.738
r_dihedral_angle_4_deg17.254
r_dihedral_angle_3_deg11.671
r_sphericity_bonded11.532
r_long_range_B_refined5.573
r_dihedral_angle_1_deg5.541
r_long_range_B_other4.812
r_scangle_other4.375
r_scbond_it3.768
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.612
r_sphericity_free35.738
r_dihedral_angle_4_deg17.254
r_dihedral_angle_3_deg11.671
r_sphericity_bonded11.532
r_long_range_B_refined5.573
r_dihedral_angle_1_deg5.541
r_long_range_B_other4.812
r_scangle_other4.375
r_scbond_it3.768
r_scbond_other3.766
r_mcangle_other2.755
r_mcangle_it2.72
r_mcbond_it2.201
r_mcbond_other2.087
r_rigid_bond_restr1.797
r_angle_refined_deg1.493
r_angle_other_deg0.851
r_chiral_restr0.083
r_bond_refined_d0.009
r_gen_planes_refined0.007
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 Atoms1691
Nucleic Acid Atoms
Solvent Atoms254
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing