3TBS
CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX THE WITH LCMV-DERIVED GP33 ALTERED PEPTIDE ligand (V3P,Y4A)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | Crystals were obtained in 1.6-1.8 M ammonium sulfate, 0.1 M Tris HCl pH 7.0-9.0 screening conditions. 4 ul of a 5mg/ml protein solution were mixed in a 4:2 ratio with the crystallization reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.32 | 62.94 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 117.84 | α = 90 |
| b = 125.12 | β = 128.15 |
| c = 101.32 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 2 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 315r | 2008-03-25 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | 0.934 | ESRF | ID14-2 |
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 | 2.49 | 49.21 | 99.9 | 0.152 | 10 | 3.9 | 40587 | 40587 | 55 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.5 | 2.61 | 99.9 | 0.83 | 2.1 | 3.9 | 5927 | ||||||||||||
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1S7U | 2.49 | 49.21 | 38455 | 38455 | 2006 | 99.62 | 0.23164 | 0.23164 | 0.22961 | 0.27044 | RANDOM | 52.417 | ||||
| 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] | |
| 0.47 | 0.37 | -0.1 | 0.09 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.408 |
| r_dihedral_angle_4_deg | 21.445 |
| r_dihedral_angle_3_deg | 19.157 |
| r_dihedral_angle_1_deg | 6.406 |
| r_scangle_it | 1.622 |
| r_angle_refined_deg | 1.341 |
| r_scbond_it | 1.036 |
| r_angle_other_deg | 0.958 |
| r_mcangle_it | 0.601 |
| r_mcbond_it | 0.318 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6220 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 147 |
| Heterogen Atoms | 22 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MxCuBE | data collection |
| MOLREP | phasing |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
