3BE1

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BDYPDB entry 3BDY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8292Crystals 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 coefficientSolvent content
3.1861.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.324α = 90
b = 115.056β = 90
c = 208.171γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.00ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.9501000.09518.55.73414934149
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.931000.6585.83328

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3BDY2.93033988171199.830.2220.2360.277RANDOM57.135
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]
-0.48-4.194.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.357
r_dihedral_angle_3_deg15.444
r_dihedral_angle_4_deg14.469
r_dihedral_angle_1_deg6.756
r_mcangle_it4.227
r_scangle_it3.741
r_mcbond_it2.728
r_scbond_it2.402
r_angle_refined_deg1.21
r_angle_other_deg0.846
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.357
r_dihedral_angle_3_deg15.444
r_dihedral_angle_4_deg14.469
r_dihedral_angle_1_deg6.756
r_mcangle_it4.227
r_scangle_it3.741
r_mcbond_it2.728
r_scbond_it2.402
r_angle_refined_deg1.21
r_angle_other_deg0.846
r_mcbond_other0.464
r_symmetry_hbond_refined0.296
r_nbd_refined0.207
r_symmetry_vdw_refined0.189
r_nbd_other0.185
r_nbtor_refined0.176
r_symmetry_vdw_other0.164
r_xyhbond_nbd_refined0.138
r_nbtor_other0.083
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7770
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms40

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection