5XD2

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


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
2.0239.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.16α = 90
b = 83.93β = 93.63
c = 43.64γ = 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
11.7543.551007.24.230580
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.841001.84.2

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 REPLACEMENTTHROUGHOUT5gg51.7543.5529013154299.980.180730.178160.22767RANDOM31.893
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]
-0.561.54-2.422.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.2
r_dihedral_angle_4_deg17.937
r_dihedral_angle_3_deg14.842
r_long_range_B_refined7.183
r_long_range_B_other7.048
r_dihedral_angle_1_deg6.997
r_scangle_other5.099
r_mcangle_it3.659
r_mcangle_other3.658
r_scbond_it3.395
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.2
r_dihedral_angle_4_deg17.937
r_dihedral_angle_3_deg14.842
r_long_range_B_refined7.183
r_long_range_B_other7.048
r_dihedral_angle_1_deg6.997
r_scangle_other5.099
r_mcangle_it3.659
r_mcangle_other3.658
r_scbond_it3.395
r_scbond_other3.385
r_mcbond_other2.545
r_mcbond_it2.544
r_angle_refined_deg1.874
r_angle_other_deg0.852
r_chiral_restr0.101
r_bond_refined_d0.016
r_gen_planes_refined0.008
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 Atoms2303
Nucleic Acid Atoms
Solvent Atoms293
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata processing
SCALAdata scaling
PHASERphasing
iMOSFLMdata reduction