9GI9 | pdb_00009gi9

Wildtype EGFR bound with (R)-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)
Type	Source	Accession Code	Details
experimental model	PDB	2EB3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	sodium tartrate, sodium acetate, ammonium chloride

Crystal Properties
Matthews coefficient	Solvent content
3.71	66.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.845	α = 90
b = 147.845	β = 90
c = 147.845	γ = 90

Symmetry
Space Group	I 2 3

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-F		2020-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000038	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	3.12	73.923	93.4	0.276	0.276	13.3	25.1		9052

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.122	3.237	47.1		3.489	3.489	1.4	26.2

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	3.12	73.923	8594	459	93.29	0.1921	0.1892	0.1924	0.2482	0.2417	RANDOM	114.775

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.104
r_dihedral_angle_3_deg	15.219
r_mcangle_it	11.445
r_dihedral_angle_4_deg	10.204
r_mcbond_it	7.471
r_mcbond_other	7.425
r_dihedral_angle_1_deg	7.38
r_angle_refined_deg	1.414
r_angle_other_deg	1.063
r_chiral_restr	0.053

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.104
r_dihedral_angle_3_deg	15.219
r_mcangle_it	11.445
r_dihedral_angle_4_deg	10.204
r_mcbond_it	7.471
r_mcbond_other	7.425
r_dihedral_angle_1_deg	7.38
r_angle_refined_deg	1.414
r_angle_other_deg	1.063
r_chiral_restr	0.053
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2464
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
PROCOR	data reduction
XSCALE	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.