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
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 300 | PEG 3450, Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.48 | 64.4 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 77.823 | α = 90 |
| b = 70.861 | β = 102.48 |
| c = 147.122 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
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 210 | M | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | CHESS BEAMLINE A1 | 0.976 | CHESS | A1 |
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 | 2.6 | 50 | 0.06 | 0.06 | 15.9 | 3.7 | 47467 | 47467 | 0.5 | ||||||||||
| 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) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 2.6 | 2.69 | 98.8 | 0.85 | 0.85 | 2 | |||||||||||||
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 | PDB ENTRY 1NQL and 1YY8 | 2.605 | 40 | 44979 | 2352 | 98.21 | 0.24187 | 0.23939 | 0.28896 | RANDOM | 33.698 | ||||||
| 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 | -1.49 | 0.81 | -3 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 38.684 |
| r_dihedral_angle_4_deg | 20.734 |
| r_dihedral_angle_3_deg | 19.83 |
| r_dihedral_angle_1_deg | 7.724 |
| r_sphericity_free | 5.854 |
| r_scangle_it | 2.562 |
| r_angle_refined_deg | 1.68 |
| r_scbond_it | 1.618 |
| r_sphericity_bonded | 1.528 |
| r_rigid_bond_restr | 1.14 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 7910 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 56 |
| Heterogen Atoms | 259 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-2000 | data collection |
| SCALEPACK | data scaling |
| MOLREP | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
