9L5X | pdb_00009l5x

Crystal structure of Klebsiella pneumoniae Enoyl-Acyl Carrier Protein Reductase (FabI) in complex with Triclosan

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1C14

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.7	293	0.1M Sodium Citrate pH 5.7, 0.1M Ammonium Sulphate, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.572	α = 90
b = 124.712	β = 110.38
c = 70.743	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 PILATUS 6M		2023-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM07	0.97951	ESRF	BM07

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	2.09	66.32	95.2	0.119	0.141	0.075	0.997	10.6	6.7		57229

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	2.09	2.2	92.2		0.663	0.779	0.445	0.884	2.4	5.8

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	2.09	66.32	54418	2782	95.12	0.16936	0.16607	0.1663	0.23389	0.2338	RANDOM	38.805

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]
-0.62		3.7	-4.89		2.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.573
r_dihedral_angle_4_deg	15.693
r_dihedral_angle_3_deg	14.4
r_dihedral_angle_1_deg	7.503
r_long_range_B_refined	6.421
r_long_range_B_other	6.405
r_scangle_other	4.508
r_mcangle_other	3.5
r_mcangle_it	3.498
r_scbond_it	3.061
r_scbond_other	3.06
r_mcbond_it	2.53
r_mcbond_other	2.523
r_angle_refined_deg	1.494
r_angle_other_deg	1.293
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7673
Nucleic Acid Atoms
Solvent Atoms	749
Heterogen Atoms	259

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
MOLREP	phasing