6M72

Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5GG5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH4.62980.2 M ammonium acetate, 0.1 M sodium acetate trihydrate, 30% w/v PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.141.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 192.029α = 90
b = 37.09β = 90
c = 44.65γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.95372ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.640.4999.40.1490.1670.0730.9835.74.942971
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.691000.5460.5460.6130.271.34.9

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 REPLACEMENTTHROUGHOUT5GG51.636.6540547214298.650.20270.20050.2448RANDOM20.223
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]
-0.790.250.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.217
r_dihedral_angle_4_deg16.455
r_dihedral_angle_3_deg15.641
r_dihedral_angle_1_deg6.326
r_angle_other_deg2.322
r_angle_refined_deg1.851
r_chiral_restr0.101
r_bond_other_d0.034
r_bond_refined_d0.015
r_gen_planes_other0.015
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.217
r_dihedral_angle_4_deg16.455
r_dihedral_angle_3_deg15.641
r_dihedral_angle_1_deg6.326
r_angle_other_deg2.322
r_angle_refined_deg1.851
r_chiral_restr0.101
r_bond_other_d0.034
r_bond_refined_d0.015
r_gen_planes_other0.015
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2299
Nucleic Acid Atoms
Solvent Atoms378
Heterogen Atoms38

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction