3EUM
A bimolecular anti-parallel-stranded Oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine BSU-6066
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1L1H | PDB ID 1L1H |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 285.15 | 2 microliter drops containing 5% v/v MPD, 0.50 mM DNA, 0.25 mM Ligand, 40 mM Potassium chloride, 5 mM Magnesium chloride, 4.1 Spermine equilibrated against 35% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.62 | α = 90 |
b = 42.307 | β = 90 |
c = 27.079 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | 105 | CCD | OXFORD ONYX CCD | Oxford diffraction Nova | 2007-08-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | OXFORD DIFFRACTION ENHANCE ULTRA | 1.540562 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.78 | 24.35 | 81.7 | 0.079 | 15.57 | 2.3 | 6576 | 5372 | 14.2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.78 | 1.93 | 39.1 | 0.28 | 1.3 | 539 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | PDB ID 1L1H | 1.78 | 24.35 | 5372 | 5106 | 238 | 81.91 | 0.2241 | 0.22174 | 0.27042 | RANDOM | 16.544 |
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] | |
-0.87 | -0.93 | 1.8 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_it | 2.055 |
r_angle_refined_deg | 1.894 |
r_scbond_it | 1.438 |
r_nbd_refined | 0.34 |
r_nbtor_refined | 0.294 |
r_symmetry_hbond_refined | 0.272 |
r_symmetry_vdw_refined | 0.153 |
r_xyhbond_nbd_refined | 0.123 |
r_metal_ion_refined | 0.082 |
r_chiral_restr | 0.066 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 506 |
Solvent Atoms | 52 |
Heterogen Atoms | 42 |
Software
Software | |
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Software Name | Purpose |
CrysalisPro | data collection |
PHASER | phasing |
REFMAC | refinement |
CrysalisPro | data reduction |
CrysalisPro | data scaling |