Experiment: 9PL0

The structure of the Fusobacterium nucleatum Enoyl-Acyl Carrier Protein Reductase (FabK) bound to an inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7L00

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	291.15	25% Jeffamine ED-2001 pH 7.0, 0.1M Sodium Citrate Tribasic pH 5.0, 8.3 uMolar of the inhibitor (final DMSO concentration 0.2 %).

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.272	α = 90
b = 194.081	β = 90.22
c = 166.818	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 EIGER2 XE 9M		2024-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 19-ID	0.9201	NSLS-II	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.25	52.27	99.59	0.3685	0.3979	0.1492	0.984	3.73	7.1		156928			33.09

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.31	98.51		2.09	2.252	0.8358	0.492	0.67	7.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.25	52.27	1.33	156293	1985	99.6	0.2139	0.2134	0.2145	0.2536	0.2541	40.04

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
f_dihedral_angle_d	15.746
f_angle_d	0.6012
f_chiral_restr	0.0422
f_plane_restr	0.0054
f_bond_d	0.0034

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28116
Nucleic Acid Atoms
Solvent Atoms	888
Heterogen Atoms	975

Software

Software
Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
PHASER	phasing
Coot	model building
DIALS	data scaling