8BT4
Ribonucleotide Reductase class Ie R2 from Mesoplasma florum, radical-lost ground state
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 294 | 175 mM calcium acetate, 100 mM ammonium sulphate and 20% (w/v) polyethylene glycol (PEG) 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 46.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 175.503 | α = 90 |
b = 53.369 | β = 108.379 |
c = 79.03 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | 100 | PIXEL | DECTRIS EIGER X 16M | 2018-11-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.0 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim I (All) | 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 | 1.35 | 48.62 | 94.89 | 0.053 | 0.999 | 14.72 | 4.3 | 144603 | 18.49 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.35 | 1.398 | 87.47 | 0.939 | 0.743 | 1.88 | 4.3 |
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 | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | FREE R-VALUE | 1.35 | 48.62 | 1.36 | 144554 | 7225 | 94.89 | 0.1444 | 0.1433 | 0.164 | 25.27 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.3345 |
f_angle_d | 0.7434 |
f_chiral_restr | 0.0696 |
f_plane_restr | 0.0066 |
f_bond_d | 0.0049 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5074 |
Nucleic Acid Atoms | |
Solvent Atoms | 590 |
Heterogen Atoms | 44 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XDS | data scaling |
PHENIX | phasing |
PHENIX | refinement |
Coot | model building |