1KB5
MURINE T-CELL RECEPTOR VARIABLE DOMAIN/FAB COMPLEX
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1VFA | PDB ENTRIES 1VFA, 1MLB, 1FLR, 1BEC |
| experimental model | PDB | 1MLB | PDB ENTRIES 1VFA, 1MLB, 1FLR, 1BEC |
| experimental model | PDB | 1FLR | PDB ENTRIES 1VFA, 1MLB, 1FLR, 1BEC |
| experimental model | PDB | 1BEC | PDB ENTRIES 1VFA, 1MLB, 1FLR, 1BEC |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7.2 | 15% PEG6000, 100MM HEPES PH 6.9-7.5, 200MM NACL, 0.1% NAN3, pH 7.2 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.5 | 54.18 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 187.31 | α = 90 |
| b = 80.95 | β = 90 |
| c = 52.08 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 120 | CCD | MIRRORS | 1996-10-13 | M | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE BM02 | ESRF | BM02 | |
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 | 2.5 | 25 | 86.7 | 0.086 | 3.1 | 24517 | 76 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 2.5 | 2.6 | 64.9 | 0.395 | 1.7 | |||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution 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 | PDB ENTRIES 1VFA, 1MLB, 1FLR, 1BEC | 2.5 | 10 | 20232 | 1048 | 0.221 | 0.219 | RANDOM | 48.9 | |||||||||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| p_scangle_it | 1.26 |
| p_mcangle_it | 1.12 |
| p_scbond_it | 0.75 |
| p_mcbond_it | 0.59 |
| p_chiral_restr | 0.213 |
| p_planar_d | 0.112 |
| p_angle_d | 0.034 |
| p_plane_restr | 0.014 |
| p_bond_d | 0.013 |
| p_angle_deg | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5172 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 266 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| XDS | data scaling |
| XSCALE | data scaling |
| AMoRE | phasing |
| REFMAC | refinement |
| XDS | data reduction |
