7DU9

Crystal structure of human Proto-oncogene tyrosine-protein kinase receptor Ret in complex with Pralsetinib


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION293.150.20 M LiCl, 0.10 M Na Acetate, pH 4.50, 2.5 M Na Formate, 5 mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.4148.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.887α = 90
b = 80.577β = 99.72
c = 79.866γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-03-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9999SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
12.3178.7297.10.0940.11910.452.727199
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.312.5697.70.440.5512.7

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 REPLACEMENTTHROUGHOUT2.3178.7226013118597.150.22040.2190.249RANDOM39.012
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]
1.540.15-0.47-1.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.635
r_dihedral_angle_4_deg15.156
r_dihedral_angle_3_deg14.102
r_dihedral_angle_1_deg6.315
r_angle_refined_deg1.551
r_angle_other_deg1.229
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.635
r_dihedral_angle_4_deg15.156
r_dihedral_angle_3_deg14.102
r_dihedral_angle_1_deg6.315
r_angle_refined_deg1.551
r_angle_other_deg1.229
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4478
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms86

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction