5GG7

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


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, 30% w/v PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.0539.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42α = 90
b = 85.35β = 94.06
c = 87.43γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2014-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54179

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
11.729.998.57.94.566623
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7996.51.84.4

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 REPLACEMENTTHROUGHOUT3FJY1.729.963220336698.440.198440.196450.23624RANDOM27.585
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]
-0.50.81-1.061.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.587
r_dihedral_angle_4_deg17.652
r_dihedral_angle_3_deg16.051
r_dihedral_angle_1_deg6.519
r_long_range_B_refined6.492
r_long_range_B_other6.313
r_scangle_other4.562
r_mcangle_it3.021
r_mcangle_other3.02
r_scbond_other2.908
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.587
r_dihedral_angle_4_deg17.652
r_dihedral_angle_3_deg16.051
r_dihedral_angle_1_deg6.519
r_long_range_B_refined6.492
r_long_range_B_other6.313
r_scangle_other4.562
r_mcangle_it3.021
r_mcangle_other3.02
r_scbond_other2.908
r_scbond_it2.903
r_mcbond_it2.096
r_mcbond_other2.092
r_angle_refined_deg1.978
r_angle_other_deg0.845
r_chiral_restr0.1
r_bond_refined_d0.015
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 Atoms4589
Nucleic Acid Atoms
Solvent Atoms642
Heterogen Atoms132

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing