6SLL | pdb_00006sll

Diaminobutyrate acetyltransferase EctA from Paenibacillus lautus in complex with its substrate L-2,4-diaminobutyric acid (DAB) and coenzyme A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6SK1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		285	0.2 M sodium fluoride, 20 % (w/v) PEG 3350, 5 mM coenzyme A, 20 mM L-2,4-diaminobutyrate

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.048	α = 90
b = 151.048	β = 90
c = 46.172	γ = 120

Symmetry
Space Group	H 3

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 PILATUS 6M-F		2017-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9762	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.05	75.53	99.2	0.048	10.43	3.59		182408

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.05	1.11			0.608	1.59

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	6SK1	1.2	75.52	116031	6191	99.46	0.1232	0.1218	0.13	0.1496	0.16	RANDOM	17.319

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]
0.03	0.02		0.03		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.953
r_sphericity_free	30.51
r_dihedral_angle_4_deg	19.694
r_sphericity_bonded	11.99
r_dihedral_angle_3_deg	11.637
r_rigid_bond_restr	7.294
r_dihedral_angle_1_deg	7.184
r_angle_refined_deg	3.024
r_angle_other_deg	1.565
r_chiral_restr	0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.953
r_sphericity_free	30.51
r_dihedral_angle_4_deg	19.694
r_sphericity_bonded	11.99
r_dihedral_angle_3_deg	11.637
r_rigid_bond_restr	7.294
r_dihedral_angle_1_deg	7.184
r_angle_refined_deg	3.024
r_angle_other_deg	1.565
r_chiral_restr	0.2
r_bond_refined_d	0.039
r_gen_planes_refined	0.018
r_gen_planes_other	0.008
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2592
Nucleic Acid Atoms
Solvent Atoms	543
Heterogen Atoms	113

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	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.