7OLY | pdb_00007oly

Structure of activin A in complex with an ActRIIB-Alk4 fusion reveal insight into activin receptor interactions

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5K59	5K59, 5MAC, 2ARV
experimental model	PDB	5MAC	5K59, 5MAC, 2ARV
experimental model	PDB	2ARV	5K59, 5MAC, 2ARV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	17.7 mg/ml complex in 20 mM HEPES, 200 mM NaCl pH 7.5. 100 + 100 nl sitting drop in a MRC 3-well plate with reservoir 0.1 M Na cacodylate pH 6.5 and 17 % (w/v) PEG 4000).

Crystal Properties
Matthews coefficient	Solvent content
3.7	66.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.375	α = 90
b = 68.375	β = 90
c = 975.538	γ = 120

Symmetry
Space Group	P 61 2 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	PIXEL	DECTRIS EIGER X 16M		2020-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.9920	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	3.26	49.25	99.9	0.317	0.054	0.999	11.7	35.3		23230

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.26	3.39	100		2.667	0.446	0.504	1.9

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5K59, 5MAC, 2ARV	3.265	49.25	23004	1209	99.7	0.2362	0.2344	0.23	0.2685	0.26	RANDOM	112.97

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]
2.9125			2.9125		-5.825

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	20.35
t_omega_torsion	3.71
t_angle_deg	0.99
t_bond_d	0.008
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5614
Nucleic Acid Atoms
Solvent Atoms	15
Heterogen Atoms	89

Software

Software
Software Name	Purpose
BUSTER	refinement
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MxCuBE	data collection
PHASER	phasing

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.