3B2U

Crystal structure of isolated domain III of the extracellular region of the epidermal growth factor receptor in complex with the Fab fragment of IMC-11F8

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YY9	PDB entries 1yy9, 1ce1, and 1dn0
experimental model	PDB	1CE1	PDB entries 1yy9, 1ce1, and 1dn0
experimental model	PDB	1DN0	PDB entries 1yy9, 1ce1, and 1dn0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5	298	12 % PEG 3350, 0.25 M ammonium acetate, 50 mM sodium acetate, pH 5.0, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.373	α = 90
b = 139.122	β = 90.02
c = 175.325	γ = 90

Symmetry
Space Group	P 1 21 1

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	ADSC QUANTUM 210		2006-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F2	0.97950	CHESS	F2

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	2.57	50	99.8	0.097	9.7	3.8	231454	231454	1	1	53

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	2.57	2.69	99		0.456	2.4	3.3	22862

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entries 1yy9, 1ce1, and 1dn0	2.58	43.07	233995	231396	11664	98.89	0.23	0.23	0.227	0.291	RANDOM	29.071

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]
-0.29		-0.04	0.39		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.399
r_dihedral_angle_4_deg	19.334
r_dihedral_angle_3_deg	17.2
r_dihedral_angle_1_deg	6.707
r_scangle_it	1.987
r_angle_refined_deg	1.439
r_scbond_it	1.193
r_mcangle_it	0.757
r_mcbond_it	0.424
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.399
r_dihedral_angle_4_deg	19.334
r_dihedral_angle_3_deg	17.2
r_dihedral_angle_1_deg	6.707
r_scangle_it	1.987
r_angle_refined_deg	1.439
r_scbond_it	1.193
r_mcangle_it	0.757
r_mcbond_it	0.424
r_nbtor_refined	0.303
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.148
r_symmetry_vdw_refined	0.145
r_symmetry_hbond_refined	0.111
r_chiral_restr	0.093
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	37083
Nucleic Acid Atoms
Solvent Atoms	1036
Heterogen Atoms	916

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

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 R01GM133198.