2Z66
Crystal structure of the VT3 hybrid of human TLR4 and hagfish VLRB.61
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2Z63 | PDB ENTRY 2Z63 |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 5.5 | 277 | 0.2M Lithium Sulfate, 0.1M Sodium Acetate, 24% PEG 4000, pH 5.50, temperature 277K, VAPOR DIFFUSION |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.02 | 59.31 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 49.787 | α = 89.86 |
| b = 67.971 | β = 89.96 |
| c = 122.779 | γ = 90.01 |
| Symmetry | |
|---|---|
| Space Group | P 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 | MIRRORS | 2007-03-09 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-3 | 1.0 | ESRF | ID14-3 |
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 | 1.9 | 50 | 93.7 | 0.09 | 2.6 | 112862 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 2Z63 | 1.9 | 20 | 120450 | 112862 | 5929 | 93.7 | 0.20966 | 0.20917 | 0.21908 | RANDOM | 13.368 | |||||
| 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] | |
| -0.19 | -0.1 | -0.1 | 0.29 | 0.03 | -0.1 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.911 |
| r_dihedral_angle_4_deg | 15.211 |
| r_dihedral_angle_3_deg | 12.099 |
| r_dihedral_angle_1_deg | 4.932 |
| r_scangle_it | 4.715 |
| r_scbond_it | 3.367 |
| r_mcangle_it | 1.877 |
| r_mcbond_it | 1.416 |
| r_angle_refined_deg | 1.098 |
| r_nbtor_refined | 0.314 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 9620 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 472 |
| Heterogen Atoms | 596 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-2000 | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
