9S3X | pdb_00009s3x

EGFR (T790M,L858R) in complex with NCL-26007

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8HV6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.15M Sodium Citrate, 0.1M TRIS pH8.5, 25% PEG400

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.18	α = 90
b = 143.18	β = 90
c = 143.18	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	173	PIXEL	DECTRIS EIGER2 XE 16M		2024-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.89842	Diamond	I03

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	2.4	50.62	100	0.169	0.173	0.037	1	16.7	41.3		19240

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)
	2.4	2.49	100		5.998	6.14	1.31	0.564	0.8	42.8

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.423	50.62	18520	952	99.075	0.192	0.1892	0.1893	0.2461	0.2459	84.954

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_lrange_it	20.217
r_dihedral_angle_3_deg	16.007
r_scangle_it	14.647
r_dihedral_angle_6_deg	14.515
r_dihedral_angle_2_deg	13.986
r_mcangle_it	11.448
r_scbond_it	10.192
r_mcbond_it	7.829
r_dihedral_angle_1_deg	6.442
r_angle_refined_deg	1.722

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	20.217
r_dihedral_angle_3_deg	16.007
r_scangle_it	14.647
r_dihedral_angle_6_deg	14.515
r_dihedral_angle_2_deg	13.986
r_mcangle_it	11.448
r_scbond_it	10.192
r_mcbond_it	7.829
r_dihedral_angle_1_deg	6.442
r_angle_refined_deg	1.722
r_nbtor_refined	0.316
r_symmetry_nbd_refined	0.236
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.21
r_symmetry_xyhbond_nbd_refined	0.179
r_chiral_restr	0.115
r_gen_planes_refined	0.007
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2585
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
pointless	data scaling
PHASER	phasing
xia2	data reduction

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.