8BWG
HRas (1-166) Y64 phosphorylation
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1WQ1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | Using a commercial crystal screen (HAMPTON RESEARCH, HR2-130) yielded a hit for monophosphorylated HRas under sitting drop conditions (drop size 600 nL) with a 1:1 ratio of protein solution (phospho-HRas 0.4 mM, RasGAP 0.4 mM, Na-HEPES 20 mM pH = 8.0, MgCl2 5 mM, NaF 20 mM) and precipitant (Na-citrate 100 mM pH = 5.6, Li2SO4 1.0 M, CaCl2 200 mM). After three rounds of microseeding well-formed single crystals were obtained using 2.0 uL sitting drops and a 1:1 ratio of protein buffer (HRas 400 uM, RasGAP 400 uM, MgCl2 5 mM, Na-HEPES 20 mM pH = 8.0, NaF 20 mM) and precipitant (Na-Citrate 100 mM pH = 5.6, Li2SO4 800 mM, CaCl2 200 mM). These were harvested using cryoprotectant (80% precipitant, 20% glycerol (v/v)) and sent for data collection. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.61 | 52.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 92.662 | α = 90 |
b = 92.662 | β = 90 |
c = 119.323 | γ = 120 |
Symmetry | |
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Space Group | H 3 2 |
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 XE 16M | 2021-01-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9763 | Diamond | I03 |
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 | 1.32 | 47.925 | 99.2 | 0.041 | 0.043 | 0.014 | 1 | 28.6 | 17.6 | 45988 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.32 | 1.34 | 1.34 | 1.535 | 0.723 | 0.577 | 7.8 |
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 (All) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.32 | 47.925 | 45983 | 2232 | 99.176 | 0.137 | 0.1354 | 0.1739 | 22.946 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.796 | -0.398 | -0.796 | 2.583 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 16.648 |
r_rigid_bond_restr | 15.682 |
r_dihedral_angle_3_deg | 14.448 |
r_dihedral_angle_2_deg | 8.675 |
r_scbond_other | 7.62 |
r_scbond_it | 7.604 |
r_scangle_it | 7.202 |
r_scangle_other | 7.192 |
r_dihedral_angle_1_deg | 6.465 |
r_lrange_it | 5.369 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1280 |
Nucleic Acid Atoms | |
Solvent Atoms | 128 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
DIALS | data reduction |
MOLREP | phasing |
Coot | model building |