8T80
Sequence specific (AATT) orientation of Hoechst molecules at two unique minor groove binding sites within a self-assembled 3D DNA lattice (4x5)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5KEK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 298 | 0.5 mL of 0.05 M Na Cacodylate pH 6.0 with 200 mM MgCl2 and 2.5 M KCl was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
6.25 | 80.33 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.503 | α = 90 |
b = 68.503 | β = 90 |
c = 59.129 | γ = 120 |
Symmetry | |
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Space Group | P 32 |
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 PILATUS3 6M | 2022-09-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.92 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 2.9 | 50 | 94.4 | 0.122 | 0.13 | 0.045 | 0.981 | 7.3 | 8.2 | 6418 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.9 | 2.95 | 66.4 | 1.348 | 1.462 | 0.553 | 0.687 | 5.7 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.91 | 41.88 | 5931 | 305 | 91.92 | 0.22023 | 0.21936 | 0.23551 | RANDOM | 113.191 |
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] | |
-0.22 | -0.11 | -0.22 | 0.73 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_long_range_B_refined | 18.143 |
r_long_range_B_other | 18.137 |
r_scangle_other | 15.347 |
r_scbond_it | 10.652 |
r_scbond_other | 10.647 |
r_angle_refined_deg | 1.829 |
r_angle_other_deg | 0.512 |
r_chiral_restr | 0.151 |
r_gen_planes_refined | 0.012 |
r_bond_other_d | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 856 |
Solvent Atoms | 6 |
Heterogen Atoms | 69 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data scaling |
HKL-2000 | data reduction |
PHASER | phasing |