4WPK

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH6.52931.6 M Sodium citrate tribasic dihydrate
Crystal Properties
Matthews coefficientSolvent content
2.0941.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.919α = 90
b = 63.473β = 112.89
c = 45.186γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.72932ESRFBM14

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
10.9823.741009.44.9115505
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.981.031002.44.5

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 DIFFRACTIONTHROUGHOUT3A7N0.9823.74109683578999.750.137460.136590.15416RANDOM12.14
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]
0.170.45-0.03-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.237
r_dihedral_angle_2_deg34.132
r_dihedral_angle_4_deg18.666
r_dihedral_angle_3_deg11.656
r_sphericity_bonded9.618
r_dihedral_angle_1_deg5.953
r_rigid_bond_restr4.81
r_long_range_B_refined4.62
r_long_range_B_other3.264
r_scangle_other2.317
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.237
r_dihedral_angle_2_deg34.132
r_dihedral_angle_4_deg18.666
r_dihedral_angle_3_deg11.656
r_sphericity_bonded9.618
r_dihedral_angle_1_deg5.953
r_rigid_bond_restr4.81
r_long_range_B_refined4.62
r_long_range_B_other3.264
r_scangle_other2.317
r_angle_refined_deg1.912
r_scbond_it1.889
r_scbond_other1.889
r_mcangle_other1.135
r_mcangle_it1.13
r_angle_other_deg0.941
r_mcbond_it0.915
r_mcbond_other0.875
r_chiral_restr0.13
r_bond_refined_d0.02
r_gen_planes_refined0.012
r_bond_other_d0.003
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1734
Nucleic Acid Atoms
Solvent Atoms347
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement