2JBZ | pdb_00002jbz

Crystal structure of the Streptomyces coelicolor holo-[Acyl-carrier-protein] Synthase (AcpS) in complex with coenzyme A at 1.6 A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		S. COELICOLOR APO- ACPS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		THE PROTEIN WAS DIALYSED IN 50 MM TRIS, 10 MM MGCL2, 10% GLYCEROL, PH 8. 2.5 MM COA WAS SOAKED INTO THE PROTEIN. THE PROTEIN WAS THEN CRYSTALLYZED IN 0.3M KSCN, 15% PEG 4K, 0.1M NACACODYLATE PH 6.5.

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.087	α = 90
b = 73.087	β = 90
c = 73.087	γ = 90

Symmetry
Space Group	P 21 3

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	MARRESEARCH		2006-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1		SRS	PX10.1

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	1.62	50	90.7	0.08	18.88	6.1		16798			18.6

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)
1	1.62	1.68	69.3		0.33	2.15	1.8

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	MOLECULAR REPLACEMENT	THROUGHOUT	S. COELICOLOR APO- ACPS	1.62	51.71	14453	771	90.6	0.189	0.187	0.19	0.215	0.22	RANDOM

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.62
r_dihedral_angle_4_deg	19.696
r_dihedral_angle_3_deg	12.879
r_dihedral_angle_1_deg	5.185
r_scangle_it	5.156
r_scbond_it	3.578
r_mcangle_it	1.866
r_angle_refined_deg	1.417
r_mcbond_it	1.061
r_nbtor_refined	0.296
r_symmetry_vdw_refined	0.251
r_nbd_refined	0.208
r_symmetry_hbond_refined	0.138
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
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_refined
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	897
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling