7NMG
Human MHC Class I, A24 Allele presenting LWM, Complex with 4C6 TCR
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2BCK | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 291 | 25% PEG 1500, 0.1M PCTP Buffer, pH 9.0 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.41 | 49 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 54.32 | α = 90 |
| b = 72.13 | β = 90 |
| c = 230.65 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2016-01-21 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.97949 | Diamond | I04 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.48 | 52.93 | 99.8 | 0.095 | 0.108 | 0.05 | 0.997 | 11.6 | 4.4 | 33057 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 2.48 | 2.58 | 99.9 | 1.31 | 1.486 | 0.69 | 0.513 | 4.4 | |||||||||||
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 | 2BCK | 2.48 | 52.93 | 31375 | 1616 | 99.7 | 0.2013 | 0.1977 | 0.271 | RANDOM | 51.78 | ||||||
| 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] | |
| 0.83 | -0.15 | -0.68 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.545 |
| r_dihedral_angle_4_deg | 19.025 |
| r_dihedral_angle_3_deg | 18.286 |
| r_dihedral_angle_1_deg | 9.396 |
| r_angle_refined_deg | 1.452 |
| r_angle_other_deg | 1.183 |
| r_chiral_restr | 0.064 |
| r_bond_refined_d | 0.011 |
| r_gen_planes_refined | 0.009 |
| r_bond_other_d | 0.002 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6598 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 112 |
| Heterogen Atoms | 42 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| Aimless | data scaling |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |
| xia2 | data reduction |
| XDS | data reduction |
