7LTR | pdb_00007ltr

Structure of the heteromeric complex between the alpha-N-methyltransferase (SonM) and a truncated construct of the RiPP precursor (SonA) (with SAM)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5N0P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	proteins at 20 mg/mL and crystallized in 100 mM Bis-Tris at pH 5.5 with 100 mM ammonium acetate and 4-7% PEG 10000

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.24	α = 90
b = 112.86	β = 97.82
c = 85.87	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 EIGER X 16M		2020-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.991840	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.75	56.43	98.3	0.983	24.88	4.29		134823

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.85			0.974

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	5N0P	1.75	56.43	128081	6742	98.33	0.1889	0.1873	0.2	0.219	0.23	RANDOM	30.189

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]
0.07		0.01	-0.01		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.561
r_dihedral_angle_4_deg	16.766
r_dihedral_angle_3_deg	14.876
r_dihedral_angle_1_deg	6.052
r_angle_other_deg	2.259
r_angle_refined_deg	1.123
r_chiral_restr	0.045
r_bond_other_d	0.035
r_gen_planes_other	0.004
r_gen_planes_refined	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.561
r_dihedral_angle_4_deg	16.766
r_dihedral_angle_3_deg	14.876
r_dihedral_angle_1_deg	6.052
r_angle_other_deg	2.259
r_angle_refined_deg	1.123
r_chiral_restr	0.045
r_bond_other_d	0.035
r_gen_planes_other	0.004
r_gen_planes_refined	0.003
r_bond_refined_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9753
Nucleic Acid Atoms
Solvent Atoms	993
Heterogen Atoms	78

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.