9DF2 | pdb_00009df2

EGFR Exon20 insertion mutant ASV bound with (S)-3-((3-chloro-2-methoxyphenyl)amino)-2-(3-((tetrahydrofuran-2-yl)methoxy)pyridin-4-yl)-1,5,6,7-tetrahydro-4H-pyrrolo[3,2-c]pyridin-4-one


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6VHP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2770.8 microliters 5 mg/mL ASV protein mixed 1:1 with 100mM MES pH 6.4, 200 mM MgCl2, 14% w/v PEG 4000. 0.2 microliters of 1M sodium fluoride then added to drop
Crystal Properties
Matthews coefficientSolvent content
2.4950.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.07α = 90
b = 106.9β = 90
c = 176.22γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XU1.0SPring-8BL45XU

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
12.545.7496.30.0630.0660.0190.99926.211.313070
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)
12.52.6800.2960.3250.130.9535.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.545.741243863296.260.198650.196370.20070.24510.2489RANDOM42.932
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]
0.671.75-2.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.015
r_dihedral_angle_4_deg14.031
r_dihedral_angle_3_deg12.447
r_dihedral_angle_1_deg5.723
r_long_range_B_refined4.556
r_long_range_B_other4.551
r_mcangle_it2.802
r_mcangle_other2.802
r_scangle_other2.364
r_mcbond_it1.565
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.015
r_dihedral_angle_4_deg14.031
r_dihedral_angle_3_deg12.447
r_dihedral_angle_1_deg5.723
r_long_range_B_refined4.556
r_long_range_B_other4.551
r_mcangle_it2.802
r_mcangle_other2.802
r_scangle_other2.364
r_mcbond_it1.565
r_mcbond_other1.562
r_scbond_it1.318
r_scbond_other1.318
r_angle_refined_deg1.161
r_angle_other_deg1.032
r_chiral_restr0.042
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms2428
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms89

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing