8T1S | pdb_00008t1s

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7LTE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	240 mM sodium malonate pH 5-5.5, 8-12% PEG 3350 at a 1-1 or 2-1 ratio of protein to mother liquor. Protein concentration is 20mg/mL.

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.39	α = 90
b = 108.73	β = 93.66
c = 59.14	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 X 6M		2022-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2	52.28	99.7	0.111	0.997	10.89	5.41		44465

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.1			0.582	1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	52.28	42244	2224	99.67	0.2045	0.20273	0.2117	0.23814	0.2443	RANDOM	24.852

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]
0.06		-0.08	-0.28		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	9.746
r_long_range_B_refined	7.407
r_long_range_B_other	7.213
r_dihedral_angle_1_deg	5.214
r_scangle_other	4.656
r_scbond_it	3.024
r_scbond_other	3.024
r_mcangle_it	2.686
r_mcangle_other	2.686
r_mcbond_it	1.857
r_mcbond_other	1.855
r_dihedral_angle_2_deg	1.641
r_angle_refined_deg	0.553
r_angle_other_deg	0.292
r_chiral_restr	0.028
r_bond_other_d	0.011
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5032
Nucleic Acid Atoms
Solvent Atoms	544
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing