6GQY
KRAS-169 Q61H GPPNHP + CH-3
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3GFT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 8-15% w/v polyethylene glycol 3350 and 0.2M Lithium citrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.49 | 50.65 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 63.531 | ¦Á = 90 |
b = 118.678 | ¦Â = 90 |
c = 156.996 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 2017-06-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) | 0.9763 | PETRA III, EMBL c/o DESY | P14 (MX2) |
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 | 2.75 | 118 | 99.8 | 0.14 | 0.16 | 0.067 | 0.997 | 16 | 10.5 | 31557 |
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 | 2.75 | 2.88 | 99.9 | 0.54 | 0.59 | 0.24 | 0.916 | 1.7 | 11 |
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 | 3GFT | 2.75 | 94.67 | 29946 | 1561 | 99.6 | 0.20682 | 0.20476 | 0.24744 | RANDOM | 44.271 |
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] | |
-0.41 | 1.78 | -1.37 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.928 |
r_dihedral_angle_3_deg | 16.579 |
r_dihedral_angle_4_deg | 12.952 |
r_long_range_B_refined | 11.013 |
r_long_range_B_other | 11.012 |
r_scangle_other | 8.084 |
r_mcangle_it | 6.103 |
r_mcangle_other | 6.103 |
r_dihedral_angle_1_deg | 5.577 |
r_scbond_other | 4.936 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7940 |
Nucleic Acid Atoms | |
Solvent Atoms | 48 |
Heterogen Atoms | 310 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
xia2 | data scaling |
PHASER | phasing |