NmHR dark state structure determined by serial femtosecond crystallography
Serial Crystallography (SX)
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 5B2N | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | LIPIDIC CUBIC PHASE | 4.5 | 293 | 50 mM sodium acetate (pH 4.5), 150 mM MgCl2, 100 mM NaCl, 34% PEG400 |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.37 | 48.15 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 104.48 | α = 90 |
b = 51.18 | β = 131.78 |
c = 78.33 | γ = 90 |
Symmetry |
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Space Group | C 1 2 1 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 293 | PIXEL | PSI JUNGFRAU 16M | | 2019-09-20 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | FREE ELECTRON LASER | SwissFEL ARAMIS BEAMLINE ESA | 1.0 | SwissFEL ARAMIS | ESA |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | High viscosity injector | injection |
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 |
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1 | 1.45 | 13.5 | 100 | 0.99 | 7.2 | 364 | | 55816 | | | 19.39 |
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) |
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1 | 1.45 | 1.48 | | | 0.55 | | | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 5B2N | 1.45 | 13.45 | 1.34 | 54641 | 2773 | 99.96 | 0.1715 | 0.1705 | 0.191 | 31.8652 |
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] |
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| | | | | |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 2057 |
Nucleic Acid Atoms | |
Solvent Atoms | 79 |
Heterogen Atoms | 195 |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
CrystFEL | data reduction |
PHASER | phasing |
PDB_EXTRACT | data extraction |
CrystFEL | data scaling |