3N85

Crystallographic trimer of HER2 extracellular regions in complex with tryptophan-rich antibody fragment

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.3	293	NaCl, Na/K-phosphate, Li-sulfate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 182.22	α = 90
b = 182.22	β = 90
c = 330.851	γ = 120

Symmetry
Space Group	P 63 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 210		2007-07-10	M	SINGLE WAVELENGTH
2	1	x-ray	110	CCD	ADSC QUANTUM 315		2007-08-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	.98	ALS	5.0.1
2	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.0	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	3.2	50	96.2	0.147	13	8.3		52459

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1S78 chain A, 1FVD chains A,B	3.2	50	50562	1636	96.35	0.20689	0.20615	0.22989	RANDOM	71.724

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]
4.23	2.12		4.23		-6.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.728
r_dihedral_angle_4_deg	15.628
r_dihedral_angle_3_deg	15.513
r_dihedral_angle_1_deg	5.755
r_mcangle_it	3.192
r_scangle_it	2.946
r_mcbond_it	1.849
r_scbond_it	1.848
r_angle_refined_deg	1.096
r_nbtor_refined	0.303
r_nbd_refined	0.192
r_symmetry_vdw_refined	0.183
r_symmetry_hbond_refined	0.134
r_xyhbond_nbd_refined	0.105
r_chiral_restr	0.073
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
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	7920
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	169

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling