7C3G

Crystal structure of human ALK2 kinase domain with R206H mutation in complex with a bicyclic pyrazole inhibitor RK-73134


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293100 mM HEPES pH 7.6-8.0, 1.5-1.6 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.5651.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.34α = 90
b = 140.259β = 90
c = 59.758γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2018-09-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.000SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
11.85099.70.1070.111118.9213.396609134.77
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.9199.11.5621.6220.7871.613.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3MTF1.80246.09866085330299.6220.1870.18510.226632.697
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]
1.837-2.2510.414
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.798
r_dihedral_angle_4_deg19.547
r_dihedral_angle_3_deg14.378
r_lrange_it7.656
r_lrange_other7.282
r_dihedral_angle_1_deg7.242
r_scangle_it4.204
r_scangle_other3.893
r_mcangle_it2.914
r_mcangle_other2.914
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.798
r_dihedral_angle_4_deg19.547
r_dihedral_angle_3_deg14.378
r_lrange_it7.656
r_lrange_other7.282
r_dihedral_angle_1_deg7.242
r_scangle_it4.204
r_scangle_other3.893
r_mcangle_it2.914
r_mcangle_other2.914
r_scbond_it2.792
r_scbond_other2.441
r_mcbond_it1.924
r_mcbond_other1.921
r_angle_refined_deg1.84
r_angle_other_deg1.436
r_nbd_refined0.212
r_symmetry_nbd_other0.186
r_nbd_other0.181
r_nbtor_refined0.173
r_symmetry_xyhbond_nbd_refined0.173
r_xyhbond_nbd_refined0.163
r_symmetry_nbd_refined0.116
r_chiral_restr0.092
r_symmetry_nbtor_other0.087
r_bond_refined_d0.014
r_gen_planes_refined0.011
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4680
Nucleic Acid Atoms
Solvent Atoms469
Heterogen Atoms171

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing