3QWQ | pdb_00003qwq

Crystal structure of the extracellular domain of the epidermal growth factor receptor in complex with an adnectin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NQL	EGFR FROM PDB ENTRY 1NQL AND ADNECTIN FROM PDB ENTRY 1FNF RESIDUES 1421-1437, 1444-1466, 1470-1491, 1502-1509
experimental model	PDB	1FNF	EGFR FROM PDB ENTRY 1NQL AND ADNECTIN FROM PDB ENTRY 1FNF RESIDUES 1421-1437, 1444-1466, 1470-1491, 1502-1509

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	293	60% Tacsimate, pH 7.0, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.82	67.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68	α = 90
b = 72.1	β = 90
c = 262	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	RAYONIX MX-300		2009-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G		APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.75	50	99.6	0.069	23.1	4.8		34285			71.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.85	100		0.552	3.1	5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	EGFR FROM PDB ENTRY 1NQL AND ADNECTIN FROM PDB ENTRY 1FNF RESIDUES 1421-1437, 1444-1466, 1470-1491, 1502-1509	2.75	49.47	34224	1058	99.38	0.204	0.202	0.21	0.246	0.25	RANDOM	64.63

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]
-3.2678			-3.4156		6.6834

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	20.5
t_omega_torsion	3.35
t_angle_deg	1.4
t_bond_d	0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	20.5
t_omega_torsion	3.35
t_angle_deg	1.4
t_bond_d	0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5359
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	237

Software

Software
Software Name	Purpose
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
BUSTER	refinement

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.