6SF3 | pdb_00006sf3

Bone morphogenetic protein 10 (BMP10) in complex with extracellular domain of activin receptor-like kinase 1 (ALK1) at 2.3 Angstrom

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6SF1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	295	0.07 M Amino acids (0.014 M DL-Glutamic acids monohydrate; 0.014 M DL-Alanine; 0.014 M Glycine; 0.014 M DL-Lysine monohydrochloride; 0.014 M DL-Serine), 0.07 M Buffer System 3 (0.07 M Tris(base)/BICINE), 35% Precipitant Mix 4 (9% v/v MPD, 9% w/v PEG 1000, 9% w/ PEG3350)

Crystal Properties
Matthews coefficient	Solvent content
3.75	67.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.269	α = 90
b = 58.269	β = 90
c = 311.435	γ = 120

Symmetry
Space Group	P 65 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 PILATUS 6M-F		2019-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	311.44	99.9	0.075	0.994	7.4	14.7		15103			46.5309023868

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38	99.8		0.635	1.6	15.1

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	THROUGHOUT	6SF1	2.3000067422	51.9058333333	1.33792944578	14963	1292	99.7832369942	0.215492606269	0.21397641611	0.21	0.243250254795	0.24	58.9737321218

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	11.810858825
f_angle_d	0.849569235906
f_chiral_restr	0.050588862781
f_bond_d	0.00685146478633
f_plane_restr	0.00593486275068

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1419
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
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.