4IZ9

Crystal structure of an acetate kinase from Mycobacterium avium bound to an unknown acid-ApCpp conjugate and manganese

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	MyavA.00640.a.A1 PS00663 at 20 mg/mL with 2 mM ApCpp and 2 mM MnCl2 against PACT screen condition A4, 0.1 M SPG buffer pH 7.0, 25% PEG 3350 and 15% ethylene glycol as cryo-protectant, crystal tracking ID 236958a4, unique puck ID lqa0-2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.89	68.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.77	α = 90
b = 95.77	β = 90
c = 141.23	γ = 90

Symmetry
Space Group	P 41 21 2

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	2012-10-08	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	1.98	50	99.7	0.116	17.92	10.2		44007		-3	34.164

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	1.98	2.26	100		0.524	6.34

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 3p4i	1.98	45.39	44007	2348	99.86	0.1741	0.1725	0.2027	RANDOM	39.2756

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]
-0.37			-0.37		0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.664
r_dihedral_angle_4_deg	19.83
r_dihedral_angle_3_deg	13.728
r_dihedral_angle_1_deg	5.981
r_mcangle_it	2.464
r_mcbond_it	1.624
r_mcbond_other	1.624
r_angle_refined_deg	1.429
r_angle_other_deg	0.806
r_chiral_restr	0.083

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.664
r_dihedral_angle_4_deg	19.83
r_dihedral_angle_3_deg	13.728
r_dihedral_angle_1_deg	5.981
r_mcangle_it	2.464
r_mcbond_it	1.624
r_mcbond_other	1.624
r_angle_refined_deg	1.429
r_angle_other_deg	0.806
r_chiral_restr	0.083
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2830
Nucleic Acid Atoms
Solvent Atoms	300
Heterogen Atoms	55

Software

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

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 R01GM133198.