8UWR

Crystal structure of human ACVR1 (ALK2) kinase in complex with compound 3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3Q4U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52931.5 M Ammonium Sulphate, 0.1 M Sodium Citrate, pH 5.6
Crystal Properties
Matthews coefficientSolvent content
1.8734.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.61α = 90
b = 66.36β = 90
c = 162.14γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMAR scanner 345 mm plateOsmic mirrors2016-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.0420930.1484.82.516767
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.042.1595.80.7031.22.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.04201595980792.030.214390.21080.28071RANDOM39.804
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]
-0.03-0.090.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.366
r_dihedral_angle_4_deg18.297
r_dihedral_angle_3_deg16.546
r_long_range_B_refined8.302
r_long_range_B_other8.183
r_dihedral_angle_1_deg6.795
r_scangle_other3.197
r_mcangle_it2.901
r_mcangle_other2.901
r_scbond_it2.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.366
r_dihedral_angle_4_deg18.297
r_dihedral_angle_3_deg16.546
r_long_range_B_refined8.302
r_long_range_B_other8.183
r_dihedral_angle_1_deg6.795
r_scangle_other3.197
r_mcangle_it2.901
r_mcangle_other2.901
r_scbond_it2.078
r_scbond_other2.077
r_mcbond_it1.771
r_mcbond_other1.77
r_angle_refined_deg1.61
r_angle_other_deg1.013
r_chiral_restr0.096
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2389
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing