9S5X | pdb_00009s5x

Crystal structure of Neisseria gonorrhoeae FabI in complex with NADH and (E)-3-((2R,3S)-3-hydroxy-2-methyl-4-oxo-2,3,4,5-tetrahydro-1H-pyrido[2,3-b][1,4]diazepin-8-yl)-N-methyl-N-((3-methylbenzofuran-2-yl)methyl)acrylamide

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	295	100mM Bicine pH9; 2.4M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.26	α = 90
b = 91.26	β = 90
c = 241.06	γ = 120

Symmetry
Space Group	P 61 2 2

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 9M		2021-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.9801	SOLEIL	PROXIMA 2

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	1.34	75.21	96.9	0.058	0.059	0.013	1	26.1	19.8		108279

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	1.34	1.445	77.7		2.06	2.114	0.472	0.655	1.6	19.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.34	75.21	102908	5371	81.48	0.168	0.1666	0.1673	0.1964	0.1968	RANDOM	20.842

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]
0.01	0.01		0.01		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.964
r_dihedral_angle_2_deg	11.478
r_dihedral_angle_1_deg	6.382
r_mcangle_it	2.522
r_angle_refined_deg	2.038
r_mcbond_it	1.896
r_mcbond_other	1.895
r_angle_other_deg	0.657
r_chiral_restr	0.098
r_bond_refined_d	0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.964
r_dihedral_angle_2_deg	11.478
r_dihedral_angle_1_deg	6.382
r_mcangle_it	2.522
r_angle_refined_deg	2.038
r_mcbond_it	1.896
r_mcbond_other	1.895
r_angle_other_deg	0.657
r_chiral_restr	0.098
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3836
Nucleic Acid Atoms
Solvent Atoms	412
Heterogen Atoms	150

Software

Software
Software Name	Purpose
REFMAC	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
autoPROC	data reduction
autoPROC	data scaling

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.