Structure of an Anti-Methotrexate CDR1-4 Graft VHH Antibody in Complex with Methotrexate
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293.15 | 0.2M Lithium Sulfate Monohydrate, 0.1M Tris. 25% w/v PEG 3,350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.4 | 48.68 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 43.669 | α = 90 |
| b = 57.605 | β = 90.27 |
| c = 131.136 | 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 | MAR 225 | 2010-07-12 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 22-BM | 0.979 | APS | 22-BM |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.5 | 20 | 99.5 | 0.076 | 8.73 | 3.4 | 37495 | 2 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | MIR | THROUGHOUT | 2.5 | 20 | 37250 | 35361 | 1859 | 98.75 | 0.23209 | 0.22955 | 0.22 | 0.27855 | 0.27 | RANDOM | 48.323 | ||||
| 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] | |
| 5.31 | 1.09 | -0.23 | -5.07 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.844 |
| r_dihedral_angle_3_deg | 19.828 |
| r_dihedral_angle_4_deg | 18.836 |
| r_dihedral_angle_1_deg | 7.884 |
| r_scangle_it | 3.264 |
| r_scbond_it | 2.375 |
| r_mcangle_it | 1.536 |
| r_angle_refined_deg | 1.518 |
| r_mcbond_it | 0.943 |
| r_chiral_restr | 0.116 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4688 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 53 |
| Heterogen Atoms | 173 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-2000 | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
