Experiment: 1S78

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N8Y	Rat ErbB2 extracellular domain (PDB code 1N8Y) and uncomplexed pertuzumab Fab (PDB code 1L7I)
experimental model	PDB	1L7I	Rat ErbB2 extracellular domain (PDB code 1N8Y) and uncomplexed pertuzumab Fab (PDB code 1L7I)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	PEG 3350, ammonium formate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4	69.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 139.412	α = 90
b = 139.412	β = 90
c = 356.873	γ = 90

Symmetry
Space Group	P 43 21 2

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 4		2001-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	1.00	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3.25	30	99.9	0.116	0.116	19.3	8.2	56393	56351		-3	97.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.25	3.37	100		0.691	0.691	3.3	8.3	5496

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Rat ErbB2 extracellular domain (PDB code 1N8Y) and uncomplexed pertuzumab Fab (PDB code 1L7I)	3.25	15	55651	52816	2835	100	0.2265	0.22655	0.22429	0.23	0.26772	0.26	SHELLS (A): 3.289 - 3.285, 3.370 - 3.366, 3.459 - 3.454, 3.559 - 3.554, 3.670 - 3.664, 3.798 - 3.791, 3.944 - 3.937, 4.117 - 4.107, 4.323 - 4.313, 4.577 - 4.564, 4.904 - 4.886, 5.345 - 5.319, 6.000 - 5.960, 7.157 - 7.073, 10.465 - 10.120	10.586

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]
2.21			2.21		-4.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.52
r_scangle_it	2.83
r_mcangle_it	2.717
r_scbond_it	1.81
r_mcbond_it	1.657
r_angle_refined_deg	1.273
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.208
r_symmetry_hbond_refined	0.176
r_xyhbond_nbd_refined	0.137

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.52
r_scangle_it	2.83
r_mcangle_it	2.717
r_scbond_it	1.81
r_mcbond_it	1.657
r_angle_refined_deg	1.273
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.208
r_symmetry_hbond_refined	0.176
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.083
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15302
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	179

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

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.