7PCN

BurG (holo) in complex with gonyenediol (14), trigonic acid (6) and DMS: Biosynthesis of cyclopropanol rings in bacterial toxins

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	0.1 M Inidazole; 10% PEG 8K, 2 mM NAD+, 5 mM MgCl2, 2 mM gonydiol (5)

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.88	α = 90
b = 76.13	β = 105.14
c = 79.11	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		2021-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.6	30	98.2	0.091	7.3	3.1		82909

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.7			0.573	1.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7PCC	1.6	30	78752	4145	98.27	0.135	0.1337	0.1594	RANDOM	17.986

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]
0.68		-0.55	-0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.011
r_dihedral_angle_4_deg	19.017
r_dihedral_angle_3_deg	12.128
r_dihedral_angle_1_deg	6.04
r_rigid_bond_restr	1.589
r_angle_refined_deg	1.442
r_angle_other_deg	1.417
r_chiral_restr	0.075
r_bond_refined_d	0.006
r_gen_planes_refined	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.011
r_dihedral_angle_4_deg	19.017
r_dihedral_angle_3_deg	12.128
r_dihedral_angle_1_deg	6.04
r_rigid_bond_restr	1.589
r_angle_refined_deg	1.442
r_angle_other_deg	1.417
r_chiral_restr	0.075
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5225
Nucleic Acid Atoms
Solvent Atoms	473
Heterogen Atoms	140

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	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.