1YY9

Structure of the extracellular domain of the epidermal growth factor receptor in complex with the Fab fragment of cetuximab/Erbitux/IMC-C225


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NQLPDB ENTRY 1NQL and 1YY8
experimental modelPDB 1YY8PDB ENTRY 1NQL and 1YY8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5300PEG 3450, Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
3.4864.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.823α = 90
b = 70.861β = 102.48
c = 147.122γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A10.976CHESSA1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.6500.060.0615.93.747467474670.5
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)RedundancyNumber Unique Reflections (All)
12.62.6998.80.850.852

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 1NQL and 1YY82.6054044979235298.210.241870.239390.28896RANDOM33.698
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]
1.54-1.490.81-3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.684
r_dihedral_angle_4_deg20.734
r_dihedral_angle_3_deg19.83
r_dihedral_angle_1_deg7.724
r_sphericity_free5.854
r_scangle_it2.562
r_angle_refined_deg1.68
r_scbond_it1.618
r_sphericity_bonded1.528
r_rigid_bond_restr1.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.684
r_dihedral_angle_4_deg20.734
r_dihedral_angle_3_deg19.83
r_dihedral_angle_1_deg7.724
r_sphericity_free5.854
r_scangle_it2.562
r_angle_refined_deg1.68
r_scbond_it1.618
r_sphericity_bonded1.528
r_rigid_bond_restr1.14
r_mcangle_it1.046
r_mcbond_it0.625
r_nbtor_refined0.319
r_nbd_refined0.241
r_symmetry_vdw_refined0.203
r_xyhbond_nbd_refined0.152
r_symmetry_hbond_refined0.118
r_chiral_restr0.109
r_bond_refined_d0.015
r_gen_planes_refined0.005
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7910
Nucleic Acid Atoms
Solvent Atoms56
Heterogen Atoms259

Software

Software
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
HKL-2000data reduction