Experiment: 5K8F

Crystal structure of Acetyl-CoA Synthetase in complex with ATP and Acetyl-AMP from Cryptococcus neoformans H99

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5IFI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	289	ACETYL COA SYNTHETASE FROM CRYPTOCOCCUS NEOFORMANS (CRNEC.00629.A.FS11.PD00402) AT 10MG/ ML (IN 10 MM TRIS, PH = 7.5, 20 MM NACL) WAS SET UP IN SPARSE CRYSTALLIZATION TRIALS AT 16C. 1MM ATP AND 1MM MGCL2 WERE ADDED TO THE PROTEIN SOLUTION AND INCUBATED FOR 5 MINUTES BEFORE SETTING UP TRIALS. CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR DIFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN/LIGAND IN WIZARD 1 AND 2 SCREEN CONDITION E8 (10% W/V PEG8,000, 0.1M NA/K PHOSPHATE PH6.2) AND CRYO-PROTECTED IN 20% ETHYLENE GLYCOL. CRYSTAL ID 271854A7 GJX4-8 APS21-ID-G), PH 6.20, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.37	α = 110.06
b = 83.92	β = 105.24
c = 101.57	γ = 87.65

Symmetry
Space Group	P 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 300 mm CCD		2016-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.978560	APS	21-ID-G

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	2.45	50	98.5	0.076	0.088	0.998	14.19	4		77299		-3	37.68

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	2.45	2.51	97.8		0.517	0.597	0.861	2.56

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5IFI	2.45	26.62	1.98	77206	1997	98.59	0.1889	0.1879	0.1879	0.2242	0.2238	52.7124

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	12.702
f_angle_d	0.467
f_chiral_restr	0.042
f_plane_restr	0.004
f_bond_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14907
Nucleic Acid Atoms
Solvent Atoms	377
Heterogen Atoms	216

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing