5IFI | pdb_00005ifi

CRYSTAL STRUCTURE OF ACETYL-COA SYNTHETASE IN COMPLEX WITH ADENOSINE-5'-PROPYLPHOSPHATE FROM CRYPTOCOCCUS NEOFORMANS H99

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RY2

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 ADENOSINE-5'- PROPYLPHOSPHATE AND COA 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 269918E8 DIT9-1 APS 21-ID-F), PH 6.20, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.46	α = 90
b = 185.55	β = 93.67
c = 84.89	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	MARMOSAIC 300 mm CCD		2016-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.9786	APS	21-ID-F

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	1.95	50	98.7	0.058	14.96	3.7		159980		-3	34.78

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	1.95	2	98.5		0.535	2.47

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1RY2	1.95	41.84	159842	8023	98.6	0.186	0.185	0.18	0.213	0.21	43.33

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	14.506
f_angle_d	0.791
f_chiral_restr	0.144
f_bond_d	0.006
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14105
Nucleic Acid Atoms
Solvent Atoms	969
Heterogen Atoms	170

Software

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

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.