Ribonucleotide Reductase class Ie R2 from Mesoplasma florum, catalytically active radical state solved by XFEL
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 | 6GP2 | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | BATCH MODE | | 294 | 50 mM calcium acetate, 20 mM ammonium sulphate and 20% (w/v) PEG 3350 |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.24 | 45.2 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 142.985 | α = 90 |
b = 46.309 | β = 112.59 |
c = 58.514 | 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 | 300 | CCD | RAYONIX MX340-HS | | 2018-12-10 | 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 | SLAC LCLS BEAMLINE MFX | 1.30177 | SLAC LCLS | MFX |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | | 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 | 35 (fs) | | | 9.5 (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 | Drop on Tape | 9 (µl/min) | undefined (µm) | | | | |
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 | 1.5 | 66.01 | 99.97 | 0.931 | 0.237 | 52.3 | 49.2 | | 56800 | | | 20.48 |
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 | 1.5 | 1.53 | 100 | | 0.344 | 0.96 | 1.5 | 19.9 | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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) | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.5 | 23.82 | 1.34 | 56747 | 2841 | 99.91 | 0.1793 | 0.1775 | 0.1782 | 0.2137 | 0.2126 | 28.84 |
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 | 21.3506 |
f_angle_d | 0.7529 |
f_chiral_restr | 0.0459 |
f_bond_d | 0.0056 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 2518 |
Nucleic Acid Atoms | |
Solvent Atoms | 134 |
Heterogen Atoms | |
Software
Software |
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Software Name | Purpose |
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cctbx.xfel | data reduction |
DIALS | data reduction |
cxi.merge | data scaling |
PHASER | phasing |
PHENIX | refinement |
Coot | model building |