3GNT

Crystal Structure of the Staphylococcus aureus Enoyl-Acyl Carrier Protein Reductase (FabI) in apo form (two molecules in AU)

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	295	15% PEG 400, 0.1M Tris pH 8.0, 4% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.099	α = 90
b = 74.462	β = 119.35
c = 70.609	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	ADSC QUANTUM 270	mirrors	2008-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 6C1	1.000	PAL/PLS	6C1

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	2.75	50	96	0.09	0.17	12.7	4.2	11436	10886	2	2	36

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	2.75	2.85	47		0.18	0.17	2.4	2.1	635

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2PD3	2.75	34.96	11436	10886	548	84.04	0.244	0.24329	0.24157	0.27823	RANDOM	36.972

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]
0.12		0.03	-0.14		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	45.602
r_dihedral_angle_3_deg	29.959
r_dihedral_angle_4_deg	27.305
r_dihedral_angle_1_deg	22.748
r_scangle_it	7.129
r_scbond_it	5.057
r_angle_refined_deg	4.26
r_mcangle_it	3.073
r_mcbond_it	2.224
r_chiral_restr	0.736

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	45.602
r_dihedral_angle_3_deg	29.959
r_dihedral_angle_4_deg	27.305
r_dihedral_angle_1_deg	22.748
r_scangle_it	7.129
r_scbond_it	5.057
r_angle_refined_deg	4.26
r_mcangle_it	3.073
r_mcbond_it	2.224
r_chiral_restr	0.736
r_symmetry_vdw_refined	0.464
r_nbd_refined	0.435
r_nbtor_refined	0.398
r_xyhbond_nbd_refined	0.297
r_bond_refined_d	0.046
r_gen_planes_refined	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3157
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

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.