3NYP
A bimolecular anti-parallel-stranded Oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine ligand containing bis-3-fluoropyrrolidine end side chains
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1L1H | PDB entry 1L1H |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 285.15 | The 5 Ul drop contained 1.2 mM quadruplex DNA, 1.2 mM ligand, 4% MPD, 4 mM potassium chloride, 4 mM magnesium chloride, 4 mM sodium chloride, 4 mM lithium sulphate, 3.2 mM spermine.4HCl and 16 mM potassium cacodylate buffer at pH 6.5. This was equilibrated against a reservoir well solution of 500 Ul of 45% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 285.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.38 | 48.22 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.8 | α = 90 |
b = 44.46 | β = 90 |
c = 28.14 | 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 | ADSC QUANTUM 315 | 2009-08-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9702 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.18 | 21.99 | 97.7 | 0.051 | 0.051 | 15.5 | 3.6 | 23982 | 23982 | 2 | 2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.18 | 1.24 | 97.8 | 0.12 | 0.12 | 5.7 | 3.5 | 3423 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | PDB entry 1L1H | 1.179 | 21.99 | 0.04 | 23275 | 23275 | 1183 | 94.59 | 0.1658 | 0.1647 | 0.1881 | Random | 14.8626 |
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] | |
1.5525 | 1.2304 | -2.7829 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 31.085 |
f_angle_d | 2.125 |
f_chiral_restr | 0.141 |
f_bond_d | 0.024 |
f_plane_restr | 0.022 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 506 |
Solvent Atoms | 177 |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |