6FZ6

Crystal Structure of a radical SAM methyltransferase from Sphaerobacter thermophilus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52940.03M Sodium fluoride; 0.03M Sodium bromide; 0.03M Sodium iodide, 0.1 M HEPES/MOPS pH 7.5, 20 % Glycerol, 10% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.0339.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.84α = 90
b = 53.14β = 90
c = 113.57γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.4257.0199.990.13180.99719.6513.07150914
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.421.441002.69080.49360.95

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONSADFREE R-VALUE1.4249.2871.34150914736399.970.16710.16610.1871
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.05
f_angle_d1.109
f_chiral_restr0.11
f_bond_d0.01
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5312
Nucleic Acid Atoms
Solvent Atoms636
Heterogen Atoms76

Software

Software
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
AutoSolphasing