7NY8
Affimer K69 - KRAS protein complex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 291 | 0.1M imidazole, 0.1M MES monohydrate, 20% w/v PEG 500 MME, 10% w/v PEG 20000, 0.12M 1,6-hexanediol, 0.12M 1,2-propanediol, 0.12M 1,4-butanediol, 0.12M 1-butanol, 0.12M 2-propanol, 0.12M 1,3-propanediol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 39.77 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.008 | α = 90 |
b = 168.775 | β = 92.7 |
c = 39.653 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 EIGER2 X 16M | 2020-10-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9795 | 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 | 1.8 | 168.77 | 100 | 0.072 | 0.078 | 0.03 | 0.999 | 19.3 | 6.9 | 47236 | 25.2 |
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 | 1.8 | 1.83 | 100 | 0.734 | 0.794 | 0.3 | 0.821 | 6.9 |
Refinement
Statistics | |||||||||||||||||||
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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 | 4OBE, 4N6T | 1.8 | 84.53 | 44810 | 2378 | 100 | 0.1568 | 0.154 | 0.17 | 0.2097 | 0.22 | RANDOM | 29.893 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
1.03 | -0.05 | -1.21 | 0.18 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.552 |
r_dihedral_angle_4_deg | 19.798 |
r_dihedral_angle_3_deg | 12.334 |
r_dihedral_angle_1_deg | 6.574 |
r_angle_refined_deg | 1.314 |
r_rigid_bond_restr | 1.304 |
r_angle_other_deg | 1.223 |
r_chiral_restr | 0.052 |
r_bond_refined_d | 0.005 |
r_gen_planes_refined | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4253 |
Nucleic Acid Atoms | |
Solvent Atoms | 258 |
Heterogen Atoms | 58 |
Software
Software | |
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Software Name | Purpose |
DIALS | data scaling |
PHASER | phasing |
REFMAC | refinement |
DIALS | data reduction |