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

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6VHP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277	0.8 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 coefficient	Solvent content
2.49	50.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.07	α = 90
b = 106.9	β = 90
c = 176.22	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2021-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.0	SPring-8	BL45XU

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.5	45.74	96.3	0.063	0.066	0.019	0.999	26.2	11.3		13070

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)	Redundancy	Number Unique Reflections (All)
1	2.5	2.6		80	0.296	0.325	0.13	0.953		5.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.5	45.74	12438	632	96.26	0.19865	0.19637	0.2007	0.2451	0.2489	RANDOM	42.932

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]
0.67			1.75		-2.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.015
r_dihedral_angle_4_deg	14.031
r_dihedral_angle_3_deg	12.447
r_dihedral_angle_1_deg	5.723
r_long_range_B_refined	4.556
r_long_range_B_other	4.551
r_mcangle_it	2.802
r_mcangle_other	2.802
r_scangle_other	2.364
r_mcbond_it	1.565
r_mcbond_other	1.562
r_scbond_it	1.318
r_scbond_other	1.318
r_angle_refined_deg	1.161
r_angle_other_deg	1.032
r_chiral_restr	0.042
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	2428
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	89

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing