7ATG
Crystal structure of Z-DNA in complex with putrescinium 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 | 4HIG |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 292 | 10%(v/v) (+/-)-2-methyl-2,4-pentanediol (MPD), 40 mM sodium cacodylate pH 6.0, 80 mM KCl, 12 mM NaCl, 14 mM putrescinium dichloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.8 | 31.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 17.97 | α = 90 |
b = 31.02 | β = 90 |
c = 43.86 | 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 PILATUS3 S 6M | 2015-06-22 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 S 6M | 2015-06-22 | 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) | 0.72930 | PETRA III, EMBL c/o DESY | P13 (MX1) |
2 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.7293 | 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 | 0.6 | 25.33 | 90.5 | 0.024 | 0.027 | 0.999 | 29.84 | 3.7 | 107989 | 5.17 |
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 | 0.6 | 0.61 | 22.6 | 0.264 | 0.368 | 0.999 | 2.88 | 1.2 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4hig | 0.6 | 25.33 | 106103 | 1876 | 90.5 | 0.0888 | 0.0877 | 0.1 | 0.095 | RANDOM | 6.26 |
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] | |
Coordinate Error | ||
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Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
3 | 141.29 | 333.73 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_angle_d | 1.56 |
s_anti_bump_dis_restr | 0.089 |
s_approx_iso_adps | 0.07 |
s_similar_adp_cmpnt | 0.061 |
s_bond_d | 0.01 |
s_from_restr_planes | 0.005 |
s_similar_dist | |
s_zero_chiral_vol | |
s_non_zero_chiral_vol | |
s_rigid_bond_adp_cmpnt |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 240 |
Solvent Atoms | 159 |
Heterogen Atoms | 7 |
Software
Software | |
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Software Name | Purpose |
SHELXL | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |