8PJL
DNA duplex forming base triplets in minor groove
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3BSE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 278 | A solution containing 20mM Na-cacodylate, 10 mM MgCl2, 0.6mM DNA was mixed in a 1:1 ratio with a solution containing 56.25% v/v (+/-)-2-methyl-2,4-pentanediol, 30 mM Na-cacodylate pH 6.0, 30 mM Na-cacodylate 3H2O, 12mM SrCl2 6H2O. Total drop volume was 400nL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.74 | 55.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.833 | α = 90 |
b = 39.833 | β = 90 |
c = 58.964 | γ = 90 |
Symmetry | |
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Space Group | P 41 |
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 | RIGAKU HyPix-6000HE | 2022-06-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | RIGAKU PhotonJet-S | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 19.65 | 99.9 | 0.15 | 0.071 | 0.99 | 9.4 | 10.7 | 6283 | 26.46 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2 | 2.05 | 1.1 | 0.79 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 2 | 18.87 | 1.34 | 6244 | 326 | 99.71 | 0.1929 | 0.1907 | 0.2353 | 33.22 |
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 | 33.0283 |
f_angle_d | 0.6321 |
f_chiral_restr | 0.0395 |
f_bond_d | 0.0041 |
f_plane_restr | 0.0032 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 550 |
Solvent Atoms | 92 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
CrysalisPro | data reduction |
Aimless | data scaling |
SHELXDE | phasing |