Experiment: 9NM0

AZ5104 (metabolite of AZD9291) in complex with WT EGFR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GS2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.1 M MES, 1.0 M sodium citrate, 0.5 mM TCEP

Crystal Properties
Matthews coefficient	Solvent content
3.47	64.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.903	α = 90
b = 145.903	β = 90
c = 145.903	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 EIGER X 16M		2025-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.979338	NSLS-II	17-ID-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.59	72.951	95.4	0.266	0.285	0.988	4.9	7.9		15446			48.46

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.591	2.636			0.407

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.59	51.58	1.36	15428	792	95.08	0.209	0.2069	0.2073	0.2471	0.2471	51.72

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
f_dihedral_angle_d	19.2912
f_angle_d	1.0055
f_chiral_restr	0.056
f_plane_restr	0.0094
f_bond_d	0.0085

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2200
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	36

Software

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