5GG5

Crystal structure of Mycobacterium smegmatis MutT1


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH6.52930.2 M ammonium sulfate, 0.1 M MES monohydrate, 30% w/v PEG monomethyl ether 5000, 0.01M TCEP hydrochloride
Crystal Properties
Matthews coefficientSolvent content
2.1843.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.45α = 90
b = 87.66β = 90
c = 101.28γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2012-11-25MSINGLE 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
11.6443.8599.411.43.641476
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.641.7396.33.63.2

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 REPLACEMENTTHROUGHOUT3FJY1.6443.8539333209499.210.158670.156640.1974RANDOM17.092
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]
-0.44-0.560.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.277
r_dihedral_angle_4_deg14.83
r_dihedral_angle_3_deg13.17
r_long_range_B_refined7.054
r_long_range_B_other6.773
r_dihedral_angle_1_deg6.33
r_scangle_other3.824
r_scbond_it2.618
r_scbond_other2.617
r_mcangle_other2.483
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.277
r_dihedral_angle_4_deg14.83
r_dihedral_angle_3_deg13.17
r_long_range_B_refined7.054
r_long_range_B_other6.773
r_dihedral_angle_1_deg6.33
r_scangle_other3.824
r_scbond_it2.618
r_scbond_other2.617
r_mcangle_other2.483
r_mcangle_it2.482
r_angle_refined_deg2.034
r_mcbond_it1.58
r_mcbond_other1.565
r_angle_other_deg0.904
r_chiral_restr0.118
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.005
r_gen_planes_other0.002
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 Atoms2310
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms172

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing