4DYM

Crystal structure of the ACVR1 kinase domain in complex with the imidazo[1,2-b]pyridazine inhibitor K00135

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H9R	pdb entry 3h9r

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293.15	1.60M MgSO4; 0.1M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.8	α = 90
b = 81.86	β = 90
c = 140.39	γ = 90

Symmetry
Space Group	C 2 2 21

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	ADSC QUANTUM 315	Kirkpatrick Baez bimorph mirror pair	2010-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9795	Diamond	I02

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	2.42	44.73	99.8	0.146	8.1	4.5	13074	13046			37.5

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	2.42	2.55	100		0.75	2	4.7	1858

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 3h9r	2.42	39.18	2	13046	12375	671	99.66	0.271	0.22268	0.21952	0.27922	RANDOM	35.896

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]
-2.53			6.58		-4.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.713
r_dihedral_angle_4_deg	17.582
r_dihedral_angle_3_deg	16.158
r_dihedral_angle_1_deg	7.837
r_angle_refined_deg	1.467
r_angle_other_deg	0.793
r_chiral_restr	0.123
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.713
r_dihedral_angle_4_deg	17.582
r_dihedral_angle_3_deg	16.158
r_dihedral_angle_1_deg	7.837
r_angle_refined_deg	1.467
r_angle_other_deg	0.793
r_chiral_restr	0.123
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2306
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	57

Software

Software
Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	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.