5GG8

Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGTP, 8-oxo-dGMP and pyrophosphate (II)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH8.52930.2 M sodium acetate trihydrate, 0.1 M TRIS hydrochloride, pH 8.5, 30% w/v PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.0339.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.05α = 90
b = 84.81β = 93.61
c = 43.52γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-11-24MSINGLE 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
11.8543.431009.54.226082
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9510024.2

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 REPLACEMENTTHROUGHOUT3FJY1.8543.4324726132799.960.178420.176130.22027RANDOM37.544
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]
-1.961.120.521.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.388
r_dihedral_angle_4_deg16.065
r_dihedral_angle_3_deg15.094
r_long_range_B_refined7.116
r_dihedral_angle_1_deg7.106
r_long_range_B_other7.054
r_scangle_other5.391
r_mcangle_it4.14
r_mcangle_other4.139
r_scbond_other3.771
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.388
r_dihedral_angle_4_deg16.065
r_dihedral_angle_3_deg15.094
r_long_range_B_refined7.116
r_dihedral_angle_1_deg7.106
r_long_range_B_other7.054
r_scangle_other5.391
r_mcangle_it4.14
r_mcangle_other4.139
r_scbond_other3.771
r_scbond_it3.769
r_mcbond_it3.045
r_mcbond_other3.044
r_angle_refined_deg1.979
r_angle_other_deg0.882
r_chiral_restr0.108
r_bond_refined_d0.017
r_gen_planes_refined0.009
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 Atoms2310
Nucleic Acid Atoms
Solvent Atoms261
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing