5XD5

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


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
2.1342.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.05α = 90
b = 64.44β = 102.59
c = 103.04γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-11-20MSINGLE 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
11.7554.2699.712.24.264503
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8498.32.13.8

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 REPLACEMENTTHROUGHOUT5gg51.7554.2661216327099.710.168240.166220.20503RANDOM33.191
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]
-0.49-0.32.75-1.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.223
r_dihedral_angle_4_deg17.966
r_dihedral_angle_3_deg13.869
r_long_range_B_refined7.327
r_long_range_B_other7.238
r_dihedral_angle_1_deg6.289
r_scangle_other5.31
r_mcangle_it3.903
r_mcangle_other3.902
r_scbond_it3.526
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.223
r_dihedral_angle_4_deg17.966
r_dihedral_angle_3_deg13.869
r_long_range_B_refined7.327
r_long_range_B_other7.238
r_dihedral_angle_1_deg6.289
r_scangle_other5.31
r_mcangle_it3.903
r_mcangle_other3.902
r_scbond_it3.526
r_scbond_other3.526
r_mcbond_it2.788
r_mcbond_other2.786
r_angle_refined_deg1.851
r_angle_other_deg0.864
r_chiral_restr0.108
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.002
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 Atoms4552
Nucleic Acid Atoms
Solvent Atoms445
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata processing
SCALAdata scaling
PHASERphasing
iMOSFLMdata reduction