3UYH
Crystal structure of an intramolecular human telomeric DNA G-quadruplex bound by the naphthalene diimide compound, MM41
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3SC8 | PDB ENTRY 3SC8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 15% PEG400, 100 mM sodium chloride, 100 mM lithium chloride, 100 mM potassium bromide, 50 mM sodium cacodylate (pH 6.5)., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.83 | 56.6 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 51.36 | ¦Á = 90 |
b = 51.36 | ¦Â = 90 |
c = 51.73 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
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 | CCD | ADSC QUANTUM 315r | 2011-12-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9795 | Diamond | I04 |
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 | 1.84 | 22.36 | 99.6 | 0.06 | 21 | 10.5 | 7126 | 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 | 1.84 | 1.88 | 100 | 0.8 | 2.9 | 10.7 |
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 ENTRY 3SC8 | 1.95 | 12 | 2807 | 5693 | 271 | 98.74 | 0.23309 | 0.23123 | 0.27496 | RANDOM | 40.963 |
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] | |
-0.03 | -0.01 | -0.03 | 0.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_angle_refined_deg | 2.008 |
r_chiral_restr | 0.079 |
r_gen_planes_refined | 0.013 |
r_bond_refined_d | 0.007 |
r_bond_other_d | |
r_angle_other_deg | |
r_dihedral_angle_1_deg | |
r_dihedral_angle_2_deg | |
r_dihedral_angle_3_deg | |
r_dihedral_angle_4_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 447 |
Solvent Atoms | 51 |
Heterogen Atoms | 63 |
Software
Software | |
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Software Name | Purpose |
CrysalisPro | data collection |
PHASER | phasing |
REFMAC | refinement |
xia2 | data scaling |
xia2 | data reduction |
SCALA | data scaling |