3MY0

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H9R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293.1516% 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 coefficientSolvent content
2.4950.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.77α = 90
b = 118.77β = 90
c = 510.791γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6Mtwo K-B pairs of bimorph type mirrors2010-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9779DiamondI24

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
12.6558.9999.90.1537.84.323388423374056
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)
12.652.7999.50.5932334027

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3H9R2.6558.992337402216231211099.710.20910.207010.24707RANDOM37.583
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]
7.817.81-15.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.2
r_dihedral_angle_4_deg18.965
r_dihedral_angle_3_deg17.571
r_dihedral_angle_1_deg6.24
r_angle_refined_deg1.27
r_angle_other_deg0.978
r_chiral_restr0.069
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_gen_planes_other0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.2
r_dihedral_angle_4_deg18.965
r_dihedral_angle_3_deg17.571
r_dihedral_angle_1_deg6.24
r_angle_refined_deg1.27
r_angle_other_deg0.978
r_chiral_restr0.069
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_gen_planes_other0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms53061
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms744

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling