7OW4
Crystal structure of HLA-A*11:01 in complex with KRAS G12D peptide (VVVGADGVGK)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2HN7 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 M Lithium sulfate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3500 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.54 | 51.63 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 117.224 | α = 90 |
b = 121.432 | β = 90 |
c = 127.863 | 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-F | 2018-11-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.9159 | Diamond | I04-1 |
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 | 1.81 | 88.05 | 100 | 0.26 | 0.269 | 0.069 | 0.998 | 8.7 | 15.1 | 166212 |
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 | 1.81 | 1.84 | 100 | 4.611 | 4.778 | 1.244 | 0.322 | 0.7 | 14.5 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2HN7 | 1.81 | 88.05 | 158094 | 8118 | 99.96 | 0.22111 | 0.21968 | 0.23 | 0.24917 | 0.25 | RANDOM | 26.136 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
0.28 | -0.73 | 0.45 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.672 |
r_dihedral_angle_4_deg | 17.277 |
r_dihedral_angle_3_deg | 13.468 |
r_dihedral_angle_1_deg | 6.832 |
r_long_range_B_refined | 4.528 |
r_long_range_B_other | 4.424 |
r_scangle_other | 1.712 |
r_angle_refined_deg | 1.482 |
r_angle_other_deg | 1.306 |
r_mcangle_it | 1.274 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 12522 |
Nucleic Acid Atoms | |
Solvent Atoms | 1009 |
Heterogen Atoms | 25 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
autoPROC | data reduction |
autoPROC | data scaling |
PHASER | phasing |