8DCA
RNA ligase RtcB from Pyrococcus horikoshii in complex with Co2+ and GTP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4ISZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 295 | apoenzyme: 0.12 mM protein, 2.1 M ammonium sulfate, 0.2 M lithium sulfate soak: 2.1 M ammonium sulfate, 0.2 M lithium sulfate, 10 mM CoCl2, 10 mM GTP soak duration: 60 min cryoprotectant: 2.0 M ammonium sulfate, 0.2 M lithium sulfate, 5 mM CoCl2, 5 mM GTP, 20 % (w/v) sucrose |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.79 | 67.52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.161 | α = 90 |
b = 138.864 | β = 90 |
c = 149.877 | 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 16M | 2021-10-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 1.6060 | APS | 24-ID-C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rpim 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 | 2.43 | 49.96 | 100 | 0.047 | 0.995 | 22.7 | 19.3 | 64578 | 64.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.43 | 2.49 | 100 | 0.337 | 0.745 | 2.1 | 19.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | FREE R-VALUE | 4ISZ | 2.43 | 49.77 | 1.35 | 64500 | 5903 | 99.99 | 0.1781 | 0.1769 | 0.2032 | 77.53 |
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 | 13.3416 |
f_angle_d | 1.0363 |
f_chiral_restr | 0.0575 |
f_plane_restr | 0.0089 |
f_bond_d | 0.0078 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7531 |
Nucleic Acid Atoms | |
Solvent Atoms | 11 |
Heterogen Atoms | 180 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |