5CXD | pdb_00005cxd

1.75 Angstrom resolution crystal structure of the apo-form acyl-carrier-protein synthase (AcpS) (acpS; purification tag off) from Staphylococcus aureus subsp. aureus COL in the I4 space group

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JM7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	295	Protein (purification tag off): 4.6 mg/mL in 10 mM Tris-HCL pH 8.3, 500 mM NaCl 5 mM BME 1 mM CaCl2 150 mM imidazole Crystallization: The PACT Suite B8(20): 200 mM Ammonium chloride 100 mM MES pH 6.0 20 % (w/v) PEG 6000 Cryo: crystallization condition

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.117	α = 90
b = 103.117	β = 90
c = 71.189	γ = 90

Symmetry
Space Group	I 4

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		2015-06-29	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	1.75	30	99.9	0.077	22.86	7.4	37637	37637			24.3

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	1.75	1.78	100		0.74	2.34	6.3

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	4JM7	1.75	29.29	35751	1880	99.85	0.17027	0.16857	0.18	0.20336	0.21	RANDOM	29.084

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]
0.5			0.5		-1.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.331
r_dihedral_angle_4_deg	11.971
r_dihedral_angle_3_deg	11.789
r_dihedral_angle_1_deg	4.096
r_angle_refined_deg	1.436
r_angle_other_deg	1.283
r_chiral_restr	0.091
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.006
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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	2913
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
BLU-MAX	data collection
PHASER	phasing
Coot	model building
HKL-2000	data reduction