3SK3 | pdb_00003sk3

Crystal structure of Salmonella typhimurium acetate kinase (AckA) with citrate bound at the dimeric interface

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	UNDER-OIL MICROBATCH	7.5	298	0.1M HEPES, 1.4M Sodium citrate, pH 7.5, UNDER-OIL MICROBATCH, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.012	α = 90
b = 78.5	β = 116.37
c = 97.48	γ = 90

Symmetry
Space Group	C 1 2 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 225 mm CCD	Bent collimating mirror and toroid	2009-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.95	ESRF	BM14

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	1.9	50	98.6	0.062	15.9	4.3		80227			41.9

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	1.9	1.97	90.4		0.786	2.18	3.4

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	PDB ENTRY 2IIR	1.9	50	75099	3977	98.42	0.1917	0.18992	0.19	0.22459	0.22	RANDOM	36.551

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]
-0.83		-0.99	1.49		-1.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.841
r_dihedral_angle_4_deg	22.701
r_dihedral_angle_3_deg	14.85
r_dihedral_angle_1_deg	5.908
r_scangle_it	3.904
r_scbond_it	2.388
r_mcangle_it	1.549
r_angle_refined_deg	1.414
r_mcbond_it	0.858
r_chiral_restr	0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.841
r_dihedral_angle_4_deg	22.701
r_dihedral_angle_3_deg	14.85
r_dihedral_angle_1_deg	5.908
r_scangle_it	3.904
r_scbond_it	2.388
r_mcangle_it	1.549
r_angle_refined_deg	1.414
r_mcbond_it	0.858
r_chiral_restr	0.098
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5804
Nucleic Acid Atoms
Solvent Atoms	442
Heterogen Atoms	29

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	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.