7TXS | pdb_00007txs

X-ray structure of the VioB N-aetyltransferase from Acinetobacter baumannii in the presence of a reaction intermediate

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	8 - 12% poly(ethylene glycol) 8000, 200 mM LiCl, 5 mM dTDP-4-amino-4,6-dideoxy-D-glucose, 5 mM CoA, and 100 mM MES (pH 6.0).

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.884	α = 90
b = 97.884	β = 90
c = 72.959	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	Bruker PHOTON II		2021-08-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER D8 QUEST	1.5418

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	1.25	50	97.7	0.061	12.2	4		70527

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	1.25	1.35	94.5		0.302	3	2.6

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	FOURIER SYNTHESIS	THROUGHOUT	7txp	1.25	29.35	66908	3619	97.69	0.1524	0.1517	0.15	0.1655	0.17	RANDOM	11.991

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.91
r_dihedral_angle_4_deg	16.925
r_dihedral_angle_3_deg	12.519
r_dihedral_angle_1_deg	7.462
r_angle_refined_deg	1.82
r_angle_other_deg	1.464
r_chiral_restr	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_gen_planes_other	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.91
r_dihedral_angle_4_deg	16.925
r_dihedral_angle_3_deg	12.519
r_dihedral_angle_1_deg	7.462
r_angle_refined_deg	1.82
r_angle_other_deg	1.464
r_chiral_restr	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_gen_planes_other	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1556
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms	89

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SAINT	data reduction
SADABS	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.