8RUJ
Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and ARN25850 after 1h soaking
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 303.15 | 100 mM magnesium acetate, 200 mM potassium chloride, 10 mM lithium chloride, 50 mM HEPES sodium, pH 7.0, 3% PEG8000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.82 | 67.81 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.57 | α = 90 |
b = 95.098 | β = 90 |
c = 227.801 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 EIGER2 X 9M | 2023-12-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID30B | 0.92 | ESRF | ID30B |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3.12 | 49.52 | 98.96 | 0.998 | 11.9 | 13.5 | 35276 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 3.12 | 3.236 | 0.316 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3.12 | 49.52 | 33507 | 1768 | 99.86 | 0.19805 | 0.19604 | 0.23617 | RANDOM | 147.217 |
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] | |
-0.78 | 8.17 | -7.39 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_long_range_B_refined | 15.565 |
r_long_range_B_other | 15.565 |
r_scangle_other | 11.663 |
r_scbond_it | 8.352 |
r_scbond_other | 8.352 |
r_angle_refined_deg | 2.472 |
r_angle_other_deg | 0.674 |
r_chiral_restr | 0.089 |
r_gen_planes_refined | 0.012 |
r_bond_refined_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 8349 |
Solvent Atoms | 63 |
Heterogen Atoms | 71 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |