5KTJ
Crystal structure of Pistol, a class of self-cleaving ribozyme
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 298.15 | 6% MPD, 0.02 M magnesium chloride, 0.02 M cobalt hexammine, 0.04 M sodium cacodylate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.76 | 55.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 85.19 | α = 90 |
b = 85.19 | β = 90 |
c = 256.54 | γ = 90 |
Symmetry | |
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Space Group | I 41 2 2 |
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 | 77.15 | PIXEL | DECTRIS PILATUS 6M-F | 2016-06-16 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 1.8445, 1.0163,1.8450 | APS | 24-ID-C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.971 | 81.27 | 99.8 | 11.87 | 17.36 | 10223 | 10205 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.971 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 2.97 | 81.27 | 9769 | 523 | 99.33 | 0.19834 | 0.19559 | 0.2 | 0.25719 | 0.25 | RANDOM | 123.508 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
0.73 | 0.73 | -1.47 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_long_range_B_refined | 15.003 |
r_long_range_B_other | 14.804 |
r_scangle_other | 10.809 |
r_scbond_it | 7.065 |
r_scbond_other | 7.056 |
r_angle_refined_deg | 2.212 |
r_angle_other_deg | 1.721 |
r_chiral_restr | 0.135 |
r_gen_planes_refined | 0.014 |
r_bond_refined_d | 0.01 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 2786 |
Solvent Atoms | 15 |
Heterogen Atoms | 165 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
SHELXDE | phasing |