7CQE

Crystal structure of the catalytic domain of the proto-oncogene tyrosine-protein kinase MER in complex with AZD-7762


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4MH7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION287Protein 40mg/mL in 20mM Tris-Cl, pH 8.0, 500mM sodium chloride, 2mM DTT. inhibitor (5 mM final concentration) overnight, Mixed 1:1 with crystallization solution (100mM Tris-Cl, pH 8.5, 4M sodium chloride)
Crystal Properties
Matthews coefficientSolvent content
2.4249.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.118α = 90
b = 69.203β = 118.42
c = 92.606γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 11C0.979PAL/PLS11C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
12.6875095.90.1030.1150.0510.98613.84.717283
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.7584.20.40.4550.210.8753.3334

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT4MH72.6943.5314760165290.230.20310.19680.2593RANDOM38.415
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]
0.01-0.060.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.037
r_dihedral_angle_4_deg19.896
r_dihedral_angle_3_deg18.123
r_dihedral_angle_1_deg6.98
r_angle_refined_deg1.66
r_angle_other_deg1.264
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.037
r_dihedral_angle_4_deg19.896
r_dihedral_angle_3_deg18.123
r_dihedral_angle_1_deg6.98
r_angle_refined_deg1.66
r_angle_other_deg1.264
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3948
Nucleic Acid Atoms
Solvent Atoms20
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing