KDO8PS Structure Determined at the EuXFEL using Segmented Flow Injection
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 | 1X8F | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | BATCH MODE | 7.3 | 293 | 8.75-12 mg/mL KDO8PS in 20 mM Tris-HCl pH=7.3, 125 mM KCl, 2 mM beta-mercaptoethanol with 16-20% w/v poly(ethylene glycol) methyl ether |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.3 | 46.47 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 118 | α = 90 |
b = 118 | β = 90 |
c = 118 | γ = 90 |
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 | AGIPD | | 2017-09-20 | 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 | EUROPEAN XFEL BEAMLINE SPB/SFX | 1.3316 | European XFEL | SPB/SFX |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | droplet in oil | injection |
Measurement |
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Diffraction ID | Pulse Duration | Pulse Repetition Rate | Focal Spot Size | Pulse Energy | Photons Per Pulse |
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1 | 100 (fs) | 320 | 300 | 9.3 (KeV) | |
Injection |
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Diffraction ID | Description | Flow Rate | Injector Diameter | Injection Power | Injector Nozzle | Filter Size | Carrier Solvent |
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1 | droplet in oil GDVN infection | 8 (µl/min) | undefined (µm) | | | | fluorinated oil |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | R Split (All) | 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 | 2.8 | 48 | 100 | 0.6367 | 0.143 | 4.61 | 184.2 | | 6888 | | | 84.6 |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 2.8 | 2.9 | 100 | | 0.4168 | 1.212 | 0.95 | 147.4 | |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1X8F | 2.8 | 48 | 6223 | 655 | 99.96 | 0.1924 | 0.1864 | 0.19 | 0.2489 | 0.24 | RANDOM | 89.936 |
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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r_dihedral_angle_2_deg | 40.625 |
r_dihedral_angle_4_deg | 22.963 |
r_dihedral_angle_3_deg | 20.237 |
r_dihedral_angle_1_deg | 7.117 |
r_angle_refined_deg | 1.471 |
r_angle_other_deg | 1.162 |
r_chiral_restr | 0.057 |
r_bond_refined_d | 0.006 |
r_gen_planes_refined | 0.005 |
r_gen_planes_other | 0.002 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_2_deg | 40.625 |
r_dihedral_angle_4_deg | 22.963 |
r_dihedral_angle_3_deg | 20.237 |
r_dihedral_angle_1_deg | 7.117 |
r_angle_refined_deg | 1.471 |
r_angle_other_deg | 1.162 |
r_chiral_restr | 0.057 |
r_bond_refined_d | 0.006 |
r_gen_planes_refined | 0.005 |
r_gen_planes_other | 0.002 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 2088 |
Nucleic Acid Atoms | |
Solvent Atoms | 2 |
Heterogen Atoms | |
Software
Software |
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Software Name | Purpose |
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REFMAC | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
CrystFEL | data reduction |
PHASER | phasing |