8A71
Crystal structure of right-handed Z-DNA containing 2'-deoxy-L-ribose in complex with the polyamine cadaverine and potassium cations at ultrahigh resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7ATG |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 292 | 1.5 MM DNA WATER SOLUTION MIXED 1:1 V/ V WITH 10% MPD, 14 MM CADAVERINE DI-HCL, 12 MM NACL, 80 MM KCL, 40 MM SODIUM CACODYLATE AND EQUILIBRATED AGAINST 80% MPD |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.7 | 27.57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 17.914 | α = 90 |
b = 31.127 | β = 90 |
c = 44.106 | 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 PILATUS 6M | 2016-11-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.7085 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 0.69 | 25.43 | 96.3 | 0.081 | 0.095 | 0.992 | 7.92 | 3.7 | 73968 | 5.963 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 0.69 | 0.74 | 0.395 | 0.486 | 0.786 | 2.02 |
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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7atg | 0.69 | 25.43 | 72088 | 1880 | 96.3 | 0.1059 | 0.1054 | 0.1283 | 7.0004 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 240 |
Solvent Atoms | 121 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
SHELX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |