7PCM | pdb_00007pcm

BurG (holo) in complex with (Z)-2,3-dihydroxy-6-methyl-hept-2-enoate (13): 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	8.5	293	0.1 M Tris; 0.8 M LiCl, 8% PEG 4K, 2 mM NAD+, 5 mM MgCl2, 2 mM 13

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.81	α = 90
b = 83.61	β = 90
c = 100.73	γ = 90

Symmetry
Space Group	P 21 21 21

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		2021-03-28	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	2.05	30	98.5	0.112	7.4	4.4		40243

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	2.05	2.15			0.596	2.4

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	7PCC	2.05	30	38214	2012	98.48	0.2053	0.2034	0.22	0.239	0.26	RANDOM	28.561

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]
-0.84			-1.87		2.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.418
r_dihedral_angle_4_deg	16.766
r_dihedral_angle_3_deg	13.56
r_dihedral_angle_1_deg	6.363
r_angle_refined_deg	1.293
r_angle_other_deg	1.173
r_rigid_bond_restr	0.67
r_chiral_restr	0.052
r_gen_planes_refined	0.004
r_bond_refined_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.418
r_dihedral_angle_4_deg	16.766
r_dihedral_angle_3_deg	13.56
r_dihedral_angle_1_deg	6.363
r_angle_refined_deg	1.293
r_angle_other_deg	1.173
r_rigid_bond_restr	0.67
r_chiral_restr	0.052
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5209
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	117

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.