3BE1 | pdb_00003be1

Dual specific bH1 Fab in complex with the extracellular domain of HER2/ErbB-2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BDY	PDB entry 3BDY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	292	Crystals of the Fab/HER2 complex were obtained by mixing protein solution (11 mg/ml protein, 25 mM Tris-HCl pH 8 and 150 mM sodium chloride) with crystallization buffer containing 25% w/v PEG2000, 0.1M MES pH 6.5. Before data collection the crystals were flash frozen in liquid nitrogen with 20% Ethylene Glycol as cryo-protectant, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
3.18	61.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.324	α = 90
b = 115.056	β = 90
c = 208.171	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	ADSC QUANTUM 315		2006-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.00	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	2.9	50	100	0.095	18.5	5.7	34149	34149

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3	100		0.658		5.8	3328

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	PDB entry 3BDY	2.9	30	33988	1711	99.83	0.222	0.236	0.22	0.277	0.28	RANDOM	57.135

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]
-0.48			-4.19		4.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.357
r_dihedral_angle_3_deg	15.444
r_dihedral_angle_4_deg	14.469
r_dihedral_angle_1_deg	6.756
r_mcangle_it	4.227
r_scangle_it	3.741
r_mcbond_it	2.728
r_scbond_it	2.402
r_angle_refined_deg	1.21
r_angle_other_deg	0.846
r_mcbond_other	0.464
r_symmetry_hbond_refined	0.296
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.189
r_nbd_other	0.185
r_nbtor_refined	0.176
r_symmetry_vdw_other	0.164
r_xyhbond_nbd_refined	0.138
r_nbtor_other	0.083
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7770
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	40

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection