3MY0

Crystal structure of the ACVRL1 (ALK1) kinase domain bound to LDN-193189

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H9R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293.15	16% PEG 3350, 0.2M Na/K PO4, 5% ethylene glycol, 2% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.77	α = 90
b = 118.77	β = 90
c = 510.791	γ = 120

Symmetry
Space Group	P 32

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	PSI PILATUS 6M	two K-B pairs of bimorph type mirrors	2010-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9779	Diamond	I24

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	2.65	58.99	99.9	0.153	7.8	4.3	233884	233740			56

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	2.65	2.79	99.5		0.593	2	3	34027

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	THROUGHOUT	3H9R	2.65	58.99	233740	221623	12110	99.71	0.2091	0.20701	0.24707	RANDOM	37.583

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]
7.81			7.81		-15.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.2
r_dihedral_angle_4_deg	18.965
r_dihedral_angle_3_deg	17.571
r_dihedral_angle_1_deg	6.24
r_angle_refined_deg	1.27
r_angle_other_deg	0.978
r_chiral_restr	0.069
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_gen_planes_other	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.2
r_dihedral_angle_4_deg	18.965
r_dihedral_angle_3_deg	17.571
r_dihedral_angle_1_deg	6.24
r_angle_refined_deg	1.27
r_angle_other_deg	0.978
r_chiral_restr	0.069
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_gen_planes_other	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	53061
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	744

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

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.