4DXE | pdb_00004dxe

2.52 Angstrom resolution crystal structure of the acyl-carrier-protein synthase (AcpS)-acyl carrier protein (ACP) protein-protein complex from Staphylococcus aureus subsp. aureus COL

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3F09	3F09 (AcpS), 1F80 (ACP)
experimental model	PDB	1F80	3F09 (AcpS), 1F80 (ACP)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	295	AcpS:ACP 1:1 molar ratio (0.33:0.33 mM) in 10 mM Tris-HCl pH 8.3, 0.5 M NaCl, 5 mM BME. The PACT suite B2 (#14: 0.1 M MIB buffer pH 5.0, 25 %(w/v) PEG1500), VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.968	α = 90
b = 102.961	β = 115.87
c = 77.298	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	MARMOSAIC 300 mm CCD	mirror	2012-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97928	APS	21-ID-D

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	2.51	30	100	0.093	13.34	3.8	36820	36820		-3	49.9

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	2.51	2.56	100		0.557	2.43	3.8	1863

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	3F09 (AcpS), 1F80 (ACP)	2.51	28.82	34837	34837	1865	98.53	0.20257	0.19971	0.2	0.25449	0.26	RANDOM	43.391

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]
-5.15		-16.9	-37.84		42.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.891
r_dihedral_angle_4_deg	11.014
r_dihedral_angle_3_deg	7.159
r_scangle_it	3.347
r_scbond_it	2.033
r_dihedral_angle_1_deg	1.661
r_mcangle_it	1.18
r_angle_refined_deg	1.156
r_angle_other_deg	0.698
r_mcbond_it	0.633

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.891
r_dihedral_angle_4_deg	11.014
r_dihedral_angle_3_deg	7.159
r_scangle_it	3.347
r_scbond_it	2.033
r_dihedral_angle_1_deg	1.661
r_mcangle_it	1.18
r_angle_refined_deg	1.156
r_angle_other_deg	0.698
r_mcbond_it	0.633
r_mcbond_other	0.134
r_chiral_restr	0.071
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8966
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	28

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	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.