6M65

Crystal structure of Mycobacterium smegmatis MutT1 in complex with GMPPNP (GDP)


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
2.141.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 192.56α = 90
b = 37.11β = 90
c = 44.79γ = 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
11.4443.6399.70.0860.0920.0340.99812.37.159223
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)
11.441.5299.70.750.750.8090.30217

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 REPLACEMENTTHROUGHOUT5GG51.4436.7656131298599.510.18310.18140.2148RANDOM16.954
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]
-0.62-0.050.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.285
r_dihedral_angle_4_deg20.43
r_dihedral_angle_3_deg12.939
r_dihedral_angle_1_deg6.416
r_angle_other_deg2.375
r_angle_refined_deg2.08
r_chiral_restr0.108
r_bond_other_d0.034
r_bond_refined_d0.018
r_gen_planes_other0.017
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.285
r_dihedral_angle_4_deg20.43
r_dihedral_angle_3_deg12.939
r_dihedral_angle_1_deg6.416
r_angle_other_deg2.375
r_angle_refined_deg2.08
r_chiral_restr0.108
r_bond_other_d0.034
r_bond_refined_d0.018
r_gen_planes_other0.017
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2258
Nucleic Acid Atoms
Solvent Atoms441
Heterogen Atoms64

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction