4JM7 | pdb_00004jm7

1.82 Angstrom resolution crystal structure of holo-(acyl-carrier-protein) synthase (acpS) from Staphylococcus aureus

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F7L	PDB ENTRY 1F7L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	The Classics II Suite, condition 22, mixed 1:1 v/v with protein sample (7.3 mg/mL, 0.25M NaCl, 5mM BME, 10mM Tris/HCl pH 8.3), pH 7.0, VAPOR DIFFUSION, temperature 295K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.394	α = 90
b = 77.398	β = 90
c = 81.5	γ = 90

Symmetry
Space Group	P 21 21 21

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 225 mm CCD	beryllium lenses	2008-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	1.82	30	98.3	0.051	24.97	5.5	37963	37963		-3

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	1.82	1.86	91.8		0.543	2.58	4.9

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	PDB ENTRY 1F7L	1.824	28.89	36019	36019	1901	98.16	0.18635	0.18431	0.19	0.22479	0.23	RANDOM	32.486

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]
-0.53			0.37		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.68
r_dihedral_angle_3_deg	10.925
r_dihedral_angle_4_deg	10.126
r_scangle_it	4.687
r_dihedral_angle_1_deg	3.844
r_scbond_it	2.949
r_mcangle_it	1.908
r_angle_refined_deg	1.289
r_mcbond_it	1.087
r_angle_other_deg	0.779

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.68
r_dihedral_angle_3_deg	10.925
r_dihedral_angle_4_deg	10.126
r_scangle_it	4.687
r_dihedral_angle_1_deg	3.844
r_scbond_it	2.949
r_mcangle_it	1.908
r_angle_refined_deg	1.289
r_mcbond_it	1.087
r_angle_other_deg	0.779
r_mcbond_other	0.343
r_chiral_restr	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2906
Nucleic Acid Atoms
Solvent Atoms	272
Heterogen Atoms

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	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.