5USJ
Crystal Structure of human KRAS G12D mutant in complex with GDPNP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 293 | 0.1 M Bis-Tris, 25% w/v PEG3350, pH 5.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.75 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 63.423 | ¦Á = 91.51 |
b = 63.491 | ¦Â = 112.63 |
c = 81.991 | ¦Ã = 115.44 |
Symmetry | |
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Space Group | P 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 | CCD | ADSC QUANTUM 315 | MIRRORS | 2013-08-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 1.075 | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.95 | 73.65 | 92.5 | 0.058 | 9.5 | 1.9 | 70797 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.95 | 2.02 | 75.5 | 0.337 | 2 | 1.9 |
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 | 1.94 | 73.65 | 67215 | 3545 | 92.11 | 0.17989 | 0.1768 | 0.23848 | RANDOM | 24.808 |
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] | |
0.15 | 0.25 | 0.15 | -0.55 | 0.15 | 0.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.323 |
r_dihedral_angle_4_deg | 20.002 |
r_dihedral_angle_3_deg | 14.514 |
r_long_range_B_refined | 7.578 |
r_long_range_B_other | 7.541 |
r_dihedral_angle_1_deg | 6.122 |
r_scangle_other | 5.238 |
r_mcangle_it | 3.309 |
r_mcangle_other | 3.309 |
r_scbond_other | 3.258 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8046 |
Nucleic Acid Atoms | |
Solvent Atoms | 725 |
Heterogen Atoms | 198 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |