9CH3

Structure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA-L63D) heteromeric complex (bound to SAH)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7LTE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5298240 mM sodium malonate pH 5.5 with 12% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1743.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52α = 90
b = 108.4β = 93.7
c = 59γ = 90.2
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.033167APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
12.319.9485.10.1380.9957.382.2748659
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.40.6050.863

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.319.9446239241984.420.277160.276060.29420.29890.3135RANDOM31.831
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]
-7.965.76-5.235.75-7.52.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.547
r_long_range_B_refined7.279
r_long_range_B_other7.276
r_dihedral_angle_1_deg5.275
r_scangle_other4.938
r_mcangle_it4.458
r_mcangle_other4.458
r_scbond_it3.247
r_scbond_other3.246
r_mcbond_it3.019
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10009
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing