8CNN
BeF3 Phospho-HRas GSA complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1QRA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | Protein buffer (phospho-HRas pY64 0.4 mM, RasGAP 0.4 mM, Na-HEPES 20 mM pH = 8.0, MgCl2 5 mM, NaF 20 mM) was mixed with precipitant in a 1:1 ratio with a total drop size of 600 nL. The precipitant solution consits of: 100 mM NaOAc, pH = 4.5, 200 mM Li2SO4, 50% PEG400 (v/v). Protein crystals were soaked in precipitant solutions containing 50-100 mM BeCl2 and subsequently flash-frozen using 20% glycerol as cryoprotectant. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 87.77 | α = 90 |
b = 87.77 | β = 90 |
c = 132.381 | 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 S 16M | 2023-02-18 | 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) | 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 | 1.48 | 49.92 | 100 | 1 | 15.8 | 20.3 | 32936 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.48 | 1.51 | 100 | 0.559 | 1.2 | 20.4 |
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 | 1.48 | 44.17 | 31254 | 1679 | 99.99 | 0.16509 | 0.16384 | 0.18838 | RANDOM | 22.508 |
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] | |
-0.15 | -0.07 | -0.15 | 0.48 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 13.174 |
r_dihedral_angle_3_deg | 12.621 |
r_long_range_B_refined | 7.393 |
r_long_range_B_other | 7.213 |
r_scangle_other | 5.945 |
r_dihedral_angle_1_deg | 5.798 |
r_scbond_it | 4.076 |
r_scbond_other | 3.99 |
r_mcangle_other | 2.826 |
r_mcangle_it | 2.82 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1385 |
Nucleic Acid Atoms | |
Solvent Atoms | 123 |
Heterogen Atoms | 16 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
Aimless | data scaling |
MOLREP | phasing |
Coot | model building |