6LL3
Crystal structure of lysozyme by fixed-target serial femtosecond crystallography
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | SMALL TUBES | 4.5 | 293.5 | sodium acetate, PEG 8000, NaCl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.83 | 32.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.98 | α = 90 |
b = 78.98 | β = 90 |
c = 38.22 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 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 | 297 | CCD | RAYONIX MX225-HS | Kirkpatrick-Baez mirror | 2019-11-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | FREE ELECTRON LASER | PAL-XFEL BEAMLINE NCI | 1.2782 | PAL-XFEL | NCI |
Serial Crystallography
Sample delivery method | ||
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Diffraction ID | Description | Sample Delivery Method |
1 | fixed target |
Fixed Target | ||||||
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Diffraction ID | Description | Sample Holding | Support Base | Motion control | Sample Solvent | |
1 | viscous medium | x-y translation stage |
Measurement | |||||
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Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
1 | 30 |
Data Reduction | |||
---|---|---|---|
Diffraction ID | Frames Indexed | Crystal Hits | Total Frames |
1 | 14264 | 24857 | 55885 |
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 | 1.8 | 72.4 | 100 | 0.9747 | 6.66 | 155.1 | 11728 |
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 | 1.8 | 1.86 | 0.7124 | 2.06 |
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 | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6IG6 | 1.85 | 55.847 | 1.35 | 10805 | 1081 | 99.99 | 0.207 | 0.2027 | 0.2462 | 22.2352 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1001 |
Nucleic Acid Atoms | |
Solvent Atoms | 82 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
CrystFEL | data reduction |
CrystFEL | data scaling |
MOLREP | phasing |