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)
TypeSourceAccession CodeDetails
experimental modelPDB 3H9Rpdb entry 3h9r

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293.151.60M MgSO4; 0.1M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.448.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.8α = 90
b = 81.86β = 90
c = 140.39γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Kirkpatrick Baez bimorph mirror pair2010-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.4244.7399.80.1468.14.5130741304637.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.422.551000.7524.71858

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 3h9r2.4239.182130461237567199.660.2710.222680.219520.27922RANDOM35.896
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]
-2.536.58-4.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.713
r_dihedral_angle_4_deg17.582
r_dihedral_angle_3_deg16.158
r_dihedral_angle_1_deg7.837
r_angle_refined_deg1.467
r_angle_other_deg0.793
r_chiral_restr0.123
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.713
r_dihedral_angle_4_deg17.582
r_dihedral_angle_3_deg16.158
r_dihedral_angle_1_deg7.837
r_angle_refined_deg1.467
r_angle_other_deg0.793
r_chiral_restr0.123
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2306
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms57

Software

Software
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling