7KNO

Crystal structure of Acetyl-CoA synthetase in complex with adenosine-5'-ethylphosphate from Cryptococcus neoformans var. grubii serotype A (H99)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	287	Optimization screen around RigakuReagents Wizard screen 1/2, condition e8: 100mM potassium / sodium phosphate dibasic pH 6.2, 200mM NaCl 13.18% (w/V) PEG 8000: CrneC.00629.a.FS11.PD00460 at 10mg/ml + ethyl-AMP + AcCoA: tray 317932 c7: cryo: 20% EG + compounds: puck: fgi6-9

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.69	α = 90
b = 184.7	β = 93.869
c = 84.84	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	RAYONIX MX-300	Beryllium Lenses	2020-09-24	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)	Rrim I (All)	CC (Half)	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	1.8	50	99.8	0.052	0.06	0.999	15.12	3.78		205272			32.568

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85	99.9		0.515	0.605	0.849	2.31	3.627

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	FREE R-VALUE	pdb entry 5ifi	1.8	46.94	1.35	205190	2070	99.84	0.164	0.1637	0.1898	0	37.97

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.8185
f_angle_d	0.9141
f_chiral_restr	0.0615
f_plane_restr	0.0095
f_bond_d	0.0082

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14797
Nucleic Acid Atoms
Solvent Atoms	1735
Heterogen Atoms	132

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
MoRDa	phasing
PHASER	phasing
PHENIX	model building
Coot	model building

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.