9CH0

Structure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA-I65W) 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 14% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1743.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.13α = 90.01
b = 108.02β = 93.41
c = 58.59γ = 89.95
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-11-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.033167APS23-ID-D

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
12.219.8486.90.1340.99510.292.2956305
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)
12.22.30.4760.935

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 REPLACEMENTTHROUGHOUT2.219.8453537276786.820.293610.29180.32280.326850.3521RANDOM26.793
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]
-7.7710.720.637.8-4.88-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.839
r_long_range_B_refined6.162
r_long_range_B_other6.158
r_dihedral_angle_1_deg5.812
r_dihedral_angle_2_deg5.811
r_scangle_other3.998
r_mcangle_it3.716
r_mcangle_other3.716
r_scbond_it2.558
r_scbond_other2.558
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9960
Nucleic Acid Atoms
Solvent Atoms170
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing