6VJF
The P-Loop K to A mutation of C. therm Vps1 GTPase-BSE
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.1 | 293 | 91 mM HEPES pH 8.1 16.7 % PEG 3,350 182 mM Sodium Acetate 3% PROPAN-2-OL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.873 | α = 90 |
b = 119.032 | β = 100.95 |
c = 84.576 | 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 EIGER X 16M | SI 111. ROSENBAUM-ROCK DOUBLE -CRYSTAL MONOCHROMATOR: LIQUID NITROGEN COOLED; SAGITALLY FOCUSING 2ND CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR | 1998-11-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 0.91299 | APS | 22-ID |
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 | 2.47 | 80.38 | 99.3 | 0.063 | 0.067 | 0.024 | 0.998 | 17.3 | 7.4 | 56551 | 55.734 |
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 | 2.47 | 2.54 | 99.5 | 0.415 | 0.445 | 0.157 | 0.954 | 5.3 | 7.8 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6DEF | 2.472 | 80.38 | 53716 | 2807 | 99.2 | 0.19093 | 0.1885 | 0.2381 | RANDOM | 49.2 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 18.2864 |
f_angle_d | 1.9656 |
f_chiral_restr | 0.1009 |
f_bond_d | 0.0158 |
f_plane_restr | 0.0098 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11199 |
Nucleic Acid Atoms | |
Solvent Atoms | 53 |
Heterogen Atoms | 132 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data processing |
Aimless | data scaling |
PHASER | phasing |