7ESS
Structure-guided studies of the Holliday junction resolvase RuvX provide novel insights into ATP-stimulated cleavage of branched DNA and RNA substrates
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1VHX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 7 | 300 | 0.1 M Bis-Tris propane, pH 7.0 and 2.4 M sodium malonate, pH 7.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.83 | 32.73 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 117.49 | α = 90 |
b = 42.58 | β = 114.45 |
c = 58.11 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS | 2021-03-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E SUPERBRIGHT | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | 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 | 1.93 | 53.477 | 99.3 | 0.067 | 0.075 | 0.034 | 13.2 | 4.7 | 19756 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.93 | 2.04 | 96.9 | 0.325 | 0.325 | 0.368 | 0.171 | 2.2 | 4.3 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1VHX | 1.93 | 52.95 | 18777 | 976 | 99.31 | 0.183 | 0.1809 | 0.2259 | RANDOM | 22.757 |
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] | |
-0.49 | -0.53 | 0.78 | 0.13 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_4_deg | 20.444 |
r_dihedral_angle_2_deg | 17.967 |
r_dihedral_angle_3_deg | 15.594 |
r_dihedral_angle_1_deg | 5.437 |
r_angle_other_deg | 3.631 |
r_angle_refined_deg | 1.484 |
r_chiral_restr | 0.071 |
r_bond_refined_d | 0.012 |
r_gen_planes_refined | 0.008 |
r_gen_planes_other | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2208 |
Nucleic Acid Atoms | |
Solvent Atoms | 185 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
iMOSFLM | data reduction |
PHASER | phasing |