7JJE
Sarcin-ricin loop with guanosine dithiophosphate residue.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3S7C | PDB ID: 3S7C |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 291 | Crystallization set-ups were made by mixing 4 uL of 350 uM RNA solution [1 mM Na 2 EDTA (pH 8.0) and 10 mM Tris-HCl (pH 8.0)] with 2 uL of a crystallization buffer composed of 3.0 M ammonium sulfate, 10 mM magnesium chloride, 10 mM manganese chloride, and 50 mM potassium 3-(N-morpholino) propanesulfonic acid (MOPS), pH 7.0 at 18 C. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.91 | 35.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 29.581 | α = 90 |
b = 29.581 | β = 90 |
c = 76.653 | γ = 90 |
Symmetry | |
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Space Group | P 43 |
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 | CCD | MARMOSAIC 300 mm CCD | 2018-04-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97857 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (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 | |||||||
1 | 1.25 | 30 | 99.5 | 0.065 | 0.028 | 40.06 | 6 | 18152 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.25 | 1.29 | 99.3 | 0.51 | 0.239 | 2.76 | 5.3 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ID: 3S7C | 1.25 | 27.6 | 17225 | 901 | 99.47 | 0.1122 | 0.1103 | 0.1478 | RANDOM | 15.641 |
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] | |
-1.63 | -1.63 | 3.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_rigid_bond_restr | 6.432 |
r_angle_refined_deg | 1.745 |
r_angle_other_deg | 1.67 |
r_chiral_restr | 0.109 |
r_gen_planes_refined | 0.028 |
r_bond_refined_d | 0.011 |
r_gen_planes_other | 0.004 |
r_bond_other_d |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 579 |
Solvent Atoms | 98 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data reduction |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data scaling |
MOLREP | phasing |