3Q4U | pdb_00003q4u

Crystal structure of the ACVR1 kinase domain in complex with LDN-193189

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H9R	pdb id: 3h9r chain A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293.15	20% PEG 3350, 0.2M ammonium citrate dibasic pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.6	α = 90
b = 98.7	β = 117.42
c = 83.85	γ = 90

Symmetry
Space Group	P 1 21 1

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	2010-01-20	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	1.82	41.88	99.2	0.086	11.6	4.3	107198	107172			24.1

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	1.82	1.92	97.8		0.734	2	4.2	15312

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: 3h9r chain A	1.82	37.22	2	107172	101787	5385	99.11	0.16557	0.16277	0.1656	0.21863	0.2195	RANDOM	22.583

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]
-0.41		0.36	0.12		0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.474
r_dihedral_angle_4_deg	20.019
r_dihedral_angle_3_deg	13.746
r_scangle_it	10.197
r_scbond_it	7.613
r_dihedral_angle_1_deg	6.156
r_mcangle_it	5.257
r_mcbond_it	3.533
r_angle_refined_deg	1.647
r_mcbond_other	1.12
r_angle_other_deg	0.867
r_chiral_restr	0.111
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9541
Nucleic Acid Atoms
Solvent Atoms	1019
Heterogen Atoms	336

Software

Software
Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling