7YUZ
Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor AP8784
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 M Ammonium iodide, 20.0 %w/v Polyethylene glycol 3,350, and 25%v/v Ethylene glycol as a cryoprotectant |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.49 | 50.55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.012 | α = 90 |
b = 66.012 | β = 90 |
c = 86.33 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | 2021-09-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.000006 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.878 | 34.45 | 94 | 0.0505 | 0.052 | 0.0121 | 0.999 | 23.58 | 19.28 | 12671 |
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) | ||||||||
1.878 | 2.079 | 69.1 | 1.8302 | 1.8843 | 0.4417 | 0.664 | 1.53 | 18.05 | 636 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.878 | 34.45 | 12671 | 623 | 69.4 | 0.2611 | 0.2589 | 0.2985 | RANDOM | 56.01 |
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] | |
0.1406 | 0.1406 | -0.2813 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 16.57 |
t_omega_torsion | 3.1 |
t_angle_deg | 0.93 |
t_bond_d | 0.008 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1409 |
Nucleic Acid Atoms | |
Solvent Atoms | 30 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
autoPROC | data processing |
XDS | data reduction |
Aimless | data scaling |
STARANISO | data scaling |
PHASER | phasing |