3GR6 | pdb_00003gr6

Crystal structure of the staphylococcus aureus enoyl-acyl carrier protein reductase (fabI) in complex with NADP and triclosan

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PD3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.3	295	10~15% PEG 400, 0.1M TRIS PH 8.0, 4% GLYCEROL, 0.005mM NADP, 0.01mM Triclosan, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.564	α = 90
b = 118.438	β = 90
c = 149.83	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 210	mirrors	2008-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 4A	1.000	PAL/PLS	4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.28	50	90.9	0.12	0.28	9.2	5.1	57719	54851	2	2	20.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.28	2.36	55		0.13	0.28	1.9	2.2	3408

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2PD3	2.28	47.09	57719	54851	2845	90.89	0.2063	0.20628	0.20328	0.21	0.26377	0.21	RANDOM	20.928

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			-0.12		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.654
r_dihedral_angle_3_deg	23.287
r_dihedral_angle_4_deg	21.4
r_dihedral_angle_1_deg	9.701
r_scangle_it	4.968
r_angle_refined_deg	4.023
r_scbond_it	3.299
r_mcangle_it	1.958
r_mcbond_it	1.191
r_symmetry_hbond_refined	0.479

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.654
r_dihedral_angle_3_deg	23.287
r_dihedral_angle_4_deg	21.4
r_dihedral_angle_1_deg	9.701
r_scangle_it	4.968
r_angle_refined_deg	4.023
r_scbond_it	3.299
r_mcangle_it	1.958
r_mcbond_it	1.191
r_symmetry_hbond_refined	0.479
r_nbtor_refined	0.34
r_symmetry_vdw_refined	0.322
r_nbd_refined	0.279
r_chiral_restr	0.234
r_xyhbond_nbd_refined	0.197
r_bond_refined_d	0.026
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7906
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	260

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.