3CE5
A bimolecular parallel-stranded human telomeric quadruplex in complex with a 3,6,9-trisubstituted acridine molecule BRACO19
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 285.15 | 1.6 mM DNA, 1.6 mM BRACO19, 200 mM ammonium sulphate, 20 mM sodium chloride, 20 mM potassium chloride, 20 mM lithium sulphate and 36 mM potassium cacodylate buffer at pH 6.5 equilibrated against 1.6 M ammonium sulphate , VAPOR DIFFUSION, HANGING DROP, temperature 285.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.81 | 56.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.338 | α = 90 |
b = 70.338 | β = 90 |
c = 34.293 | γ = 90 |
Symmetry | |
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Space Group | I 4 |
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 | IMAGE PLATE | RIGAKU RAXIS IV | mirrors | 2008-01-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 |
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 | 2.5 | 35.17 | 99.7 | 0.065 | 9.8 | 2.9 | 3003 | 2994 | 3 | 58.2 |
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 | 2.5 | 2.59 | 100 | 0.31 | 2.4 | 2.8 | 291 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB Entry 1K8P | 2.5 | 35.17 | 2992 | 2852 | 140 | 100 | 0.18446 | 0.18446 | 0.18298 | 0.21341 | RANDOM | 23.482 |
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] | |
2.08 | 2.08 | -4.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_it | 3.864 |
r_scbond_it | 2.845 |
r_angle_refined_deg | 2.813 |
r_nbtor_refined | 0.342 |
r_nbd_refined | 0.306 |
r_xyhbond_nbd_refined | 0.207 |
r_symmetry_hbond_refined | 0.196 |
r_symmetry_vdw_refined | 0.193 |
r_metal_ion_refined | 0.162 |
r_chiral_restr | 0.115 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 502 |
Solvent Atoms | 54 |
Heterogen Atoms | 46 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrystalClear | data collection |
d*TREK | data reduction |
d*TREK | data scaling |
PHASER | phasing |