Crystal structure of human Schlafen 5 N'-terminal domain (SLFN5-N) involved in ssRNA cleaving and DNA binding
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 | 5YD0 | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 277.15 | 100 mM Tris, pH 7.5, 80 mM magnesium chloride, 1.6 M ammonium sulfate |
Crystal Properties |
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Matthews coefficient | Solvent content |
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4.55 | 72.95 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 211.86 | α = 90 |
b = 156.442 | β = 110.382 |
c = 131.459 | 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 | 87.15 | PIXEL | DECTRIS PILATUS3 6M | | 2019-06-27 | M | MAD |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | SYNCHROTRON | SSRF BEAMLINE BL19U1 | 0.9785 | SSRF | BL19U1 |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | | fixed target |
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 | 3.294 | 50 | 90.2 | 1 | 13.5 | 6.8 | | 43847 | | | 80 |
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 | 3.3 | 3.61 | | | 0.731 | | | |
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 | FREE R-VALUE | 5YD0 | 3.29477066393 | 41.0761808916 | 1.34999900373 | 43638 | 2162 | 71.9161489148 | 0.203555713424 | 0.201355733206 | 0.247153773675 | 70 |
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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| | | | | |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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f_dihedral_angle_d | 3.23155903385 |
f_angle_d | 0.758545511386 |
f_chiral_restr | 0.0462753104805 |
f_plane_restr | 0.00398805901482 |
f_bond_d | 0.0028929713363 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 14069 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 6 |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
REFMAC | refinement |
XDS | data reduction |
STARANISO | data scaling |
PHASER | phasing |