4IJN

Crystal structure of an acetate kinase from Mycobacterium smegmatis bound to AMP and sulfate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	289	MysmA.00640.a.A1 PS00601 at 20 mg/mL with 2 mM AMP and 2 mM MnCl2 against JCSG+ condition H7, 25% PEG 3350, 0.1 M BisTris, 0.2 M ammonium sulfate with 15% ethylene glycol as cryo-protectant, crystal tracking ID 238414h7, unique puck ID gpy2-6, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.43	α = 90
b = 81.91	β = 96.51
c = 95.4	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	RIGAKU SATURN 944+	VariMax	2012-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	1.7	50	97.9	0.045	20.66	4.6	93194	91223		-3	23.913

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	1.7	1.74	90.2		0.29	3.22

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3r9p	1.7	45.74	91201	4566	97.89	0.1747	0.1733	0.2015	RANDOM	19.5464

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]
-0.8		-0.67	0.43		0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.396
r_dihedral_angle_4_deg	18.301
r_dihedral_angle_3_deg	11.906
r_dihedral_angle_1_deg	6.414
r_angle_refined_deg	1.484
r_mcangle_it	1.275
r_mcbond_it	0.777
r_mcbond_other	0.776
r_angle_other_deg	0.775
r_chiral_restr	0.084

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.396
r_dihedral_angle_4_deg	18.301
r_dihedral_angle_3_deg	11.906
r_dihedral_angle_1_deg	6.414
r_angle_refined_deg	1.484
r_mcangle_it	1.275
r_mcbond_it	0.777
r_mcbond_other	0.776
r_angle_other_deg	0.775
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5570
Nucleic Acid Atoms
Solvent Atoms	697
Heterogen Atoms	68

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.