6M69

Crystal structure of Mycobacterium smegmatis MutT1 in complex with GMPPCP (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 = 192.65α = 90
b = 37.08β = 90
c = 44.8γ = 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
11.536.741000.0870.0960.0410.9979.55.452698
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)
11.51.581000.610.610.6760.2881.25.4

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 REPLACEMENTTHROUGHOUT5GG51.532.8249683266799.430.19010.18840.2226RANDOM18.106
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]
-0.72-0.030.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.815
r_dihedral_angle_4_deg17.639
r_dihedral_angle_3_deg12.726
r_dihedral_angle_1_deg6.274
r_angle_other_deg2.367
r_angle_refined_deg1.983
r_chiral_restr0.11
r_bond_other_d0.034
r_bond_refined_d0.017
r_gen_planes_other0.016
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.815
r_dihedral_angle_4_deg17.639
r_dihedral_angle_3_deg12.726
r_dihedral_angle_1_deg6.274
r_angle_other_deg2.367
r_angle_refined_deg1.983
r_chiral_restr0.11
r_bond_other_d0.034
r_bond_refined_d0.017
r_gen_planes_other0.016
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2248
Nucleic Acid Atoms
Solvent Atoms383
Heterogen Atoms46

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction