5XD1

Crystal structure of Mycobacterium smegmatis MutT1 in complex with Ap5A, ATP and magnesium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5GG5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH8.52930.2M sodium acetate trihydrate, 0.1M Tris-HCl pH 8.5, 30%(w/v) PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.0239.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.21α = 90
b = 83.87β = 93.24
c = 43.65γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2016-04-13MSINGLE 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
11.643.5896.911438776
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6981.52.43

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 REPLACEMENTTHROUGHOUT5gg51.643.5836787193696.790.175960.174230.20903RANDOM29.976
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]
-0.831.55-1.712.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.568
r_dihedral_angle_4_deg17.813
r_dihedral_angle_3_deg13.738
r_long_range_B_refined6.68
r_long_range_B_other6.508
r_dihedral_angle_1_deg6.218
r_scangle_other4.462
r_mcangle_it3.209
r_mcangle_other3.208
r_scbond_it2.936
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.568
r_dihedral_angle_4_deg17.813
r_dihedral_angle_3_deg13.738
r_long_range_B_refined6.68
r_long_range_B_other6.508
r_dihedral_angle_1_deg6.218
r_scangle_other4.462
r_mcangle_it3.209
r_mcangle_other3.208
r_scbond_it2.936
r_scbond_other2.926
r_mcbond_it2.118
r_mcbond_other2.108
r_angle_refined_deg1.787
r_angle_other_deg0.814
r_chiral_restr0.096
r_bond_refined_d0.013
r_gen_planes_refined0.007
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 Atoms2305
Nucleic Acid Atoms
Solvent Atoms342
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata processing
SCALAdata scaling
PHASERphasing
iMOSFLMdata reduction