3GNS | pdb_00003gns

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

X-RAY DIFFRACTION

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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	8.5	295	10~15% PEG 400, 0.1M Tris pH 8.3~8.5, 4% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.877	α = 90
b = 74.716	β = 90
c = 110.652	γ = 90

Symmetry
Space Group	I 2 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	CCD	ADSC QUANTUM 270		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	2.7	50	98	0.08	0.28	19	8	7634	7261	2	2	43

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	2.7	2.8	56		0.13	0.28	2.95	3.4	451

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 (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	2.706	37.66	7261	7261	347	91.81	0.21476	0.21099	0.22	0.28857	0.29	RANDOM	42.514

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]
-0.3			-0.5		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.95
r_dihedral_angle_4_deg	31.784
r_dihedral_angle_3_deg	26.358
r_dihedral_angle_1_deg	14.036
r_scangle_it	7.319
r_scbond_it	4.598
r_angle_refined_deg	3.86
r_mcangle_it	3.239
r_mcbond_it	1.765
r_symmetry_hbond_refined	0.979
r_symmetry_vdw_refined	0.447
r_nbtor_refined	0.37
r_nbd_refined	0.366
r_chiral_restr	0.309
r_xyhbond_nbd_refined	0.282
r_metal_ion_refined	0.189
r_bond_refined_d	0.048
r_gen_planes_refined	0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1704
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	1

Software

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