3Q4T | pdb_00003q4t

Crystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with dorsomorphin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QLU	pdb id 2qlu

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.8	293.15	28% PEG 3350, 0.2M LiSO4, 0.1M Tris, pH 8.8, 10% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.1	α = 90
b = 110.1	β = 90
c = 206.911	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	CCD	ADSC Q315 3x3 CCD	Kirkpatrick Baez bimorph mirror pair	2010-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	1.96	48.6	99.9	0.112	11.2	7	53883	53760			26.6

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	1.96	2.07	100		0.783	2.3	7.2	7727

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 (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	pdb id 2qlu	1.96	45.47	2	53760	51027	2733	99.8	0.17124	0.16847	0.17	0.22301	0.23	RANDOM	24.429

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]
0.83	0.42		0.83		-1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.943
r_dihedral_angle_4_deg	17.193
r_dihedral_angle_3_deg	13.573
r_scangle_it	9.781
r_scbond_it	7.176
r_dihedral_angle_1_deg	6.32
r_mcangle_it	4.46
r_mcbond_it	2.974
r_angle_refined_deg	1.561
r_angle_other_deg	0.975

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.943
r_dihedral_angle_4_deg	17.193
r_dihedral_angle_3_deg	13.573
r_scangle_it	9.781
r_scbond_it	7.176
r_dihedral_angle_1_deg	6.32
r_mcangle_it	4.46
r_mcbond_it	2.974
r_angle_refined_deg	1.561
r_angle_other_deg	0.975
r_mcbond_other	0.96
r_chiral_restr	0.099
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4857
Nucleic Acid Atoms
Solvent Atoms	496
Heterogen Atoms	177

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.