2Z6J | pdb_00002z6j

Crystal Structure of S. pneumoniae Enoyl-Acyl Carrier Protein Reductase (FabK) in Complex with an Inhibitor

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z6I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	277	8-15% PEG 1000, 8-15% MPD, 0.1M MES pH 5.5-7.0, 0.1M ammonium chloride, 0.2M calcium chloride, 5mM dithiothreitol , VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.63	α = 90
b = 126.485	β = 112.04
c = 53.522	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	CCD	RIGAKU JUPITER 210	A fixed exit Si double crystal monochromator followed byStandard double crystal monochromator and Rh-coated downward-deflection mirror with a typical glancing angle of 3.7 mrad.	2005-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32B2	1.0000	SPring-8	BL32B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.3	29.08	91.9	0.083	9.2	3		25448			27.024

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.38	90		0.163	4.5	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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		THROUGHOUT	2Z6I	2.3	29.08	24154	1288	91.86	0.25226	0.24946	0.25	0.30638	0.3	RANDOM	23.443

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]
-0.52		-2.62	-2.73		1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.865
r_dihedral_angle_3_deg	16.873
r_dihedral_angle_4_deg	15.084
r_dihedral_angle_1_deg	5.486
r_scangle_it	1.74
r_angle_refined_deg	1.216
r_scbond_it	1.092
r_mcangle_it	0.756
r_mcbond_it	0.433
r_symmetry_hbond_refined	0.32
r_nbtor_refined	0.294
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.188
r_xyhbond_nbd_refined	0.142
r_metal_ion_refined	0.132
r_chiral_restr	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.003
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	4507
Nucleic Acid Atoms
Solvent Atoms	80
Heterogen Atoms	132

Software

Software
Software Name	Purpose
REFMAC	refinement
BSS	data collection
CrystalClear	data reduction
CrystalClear	data scaling