7PCL | pdb_00007pcl

BurG (holo) in complex with 2-hydroxy-2-(hydroxy(isopropyl)amino)acetate (11): Biosynthesis of cyclopropanolrings 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		293	0.1 M Tris; 0.8 M LiCl, 8% PEG 4K, 2 mM NADH, 5 mM MgCl2, 2 mM 11

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.71	α = 90
b = 84.04	β = 90
c = 101.83	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 EIGER2 X 16M		2020-11-08	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	97.8	0.097	8.5	3.8		40538

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			0.558	3.1

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	38498	2026	97.78	0.1895	0.188	0.2	0.2181	0.22	RANDOM	23.579

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]
-3.23			-0.7		3.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.12
r_dihedral_angle_4_deg	18.093
r_dihedral_angle_3_deg	13.523
r_dihedral_angle_1_deg	6.076
r_angle_refined_deg	1.255
r_angle_other_deg	1.151
r_rigid_bond_restr	0.367
r_chiral_restr	0.046
r_gen_planes_refined	0.003
r_bond_refined_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.12
r_dihedral_angle_4_deg	18.093
r_dihedral_angle_3_deg	13.523
r_dihedral_angle_1_deg	6.076
r_angle_refined_deg	1.255
r_angle_other_deg	1.151
r_rigid_bond_restr	0.367
r_chiral_restr	0.046
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
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	220
Heterogen Atoms	112

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.