3B2V

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

X-RAY DIFFRACTION

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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	6.5	298	12 % PEG 3350, IM NaCl, 50 mM MES, pH 6.5, vapor diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.09	60.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.743	α = 90
b = 266.242	β = 90
c = 156.381	γ = 90

Symmetry
Space Group	C 2 2 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	ADSC QUANTUM 210		2005-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.9	CHESS	A1

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	3.3	50	100	0.188	5.6	6	21995	21995

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	3.3	3.42	100		0.58	3.1	6.2

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entries 1yy9, 1ce1, and 1dn0	3.3	41.04	21867	20747	1120	99.14	0.286	0.28187	0.36715	RANDOM	60.921

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]
-2.8			10.75		-7.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	45.473
r_dihedral_angle_3_deg	26.099
r_dihedral_angle_4_deg	21.275
r_dihedral_angle_1_deg	12.202
r_scangle_it	3.456
r_angle_refined_deg	2.647
r_scbond_it	2.025
r_mcangle_it	1.466
r_mcbond_it	0.794
r_symmetry_vdw_refined	0.372
r_nbd_refined	0.343
r_nbtor_refined	0.343
r_xyhbond_nbd_refined	0.267
r_symmetry_hbond_refined	0.169
r_chiral_restr	0.161
r_bond_refined_d	0.022
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5524
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	121

Software

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