3CCO
Structural adaptation and conservation in quadruplex-drug recognition
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1KF1 | PDB ENTRY 1KF1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 283 | 300mM sodium chloride, 50mM sodium cacodylate pH 6.5, 30% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.14 | 60.84 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 61.35 | ¦Á = 90 |
b = 61.35 | ¦Â = 90 |
c = 43.63 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 64 2 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 | 100 | CCD | ADSC QUANTUM 210 | MONOCHROMATOR | 2007-10-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.9785 | ESRF | ID14-1 |
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 | 1.97 | 22.69 | 98.9 | 0.056 | 23.3 | 10 | 3739 | 3697 | 33 |
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) | |||||||||||
1.97 | 2.04 | 100 | 0.134 | 10.8 | 10.8 | 359 |
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 1KF1 | 2.2 | 10 | 2520 | 2520 | 123 | 98.8 | 0.25664 | 0.25664 | 0.25436 | 0.30275 | RANDOM | 21.26 |
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] | |
1.39 | 0.7 | 1.39 | -2.09 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_it | 3.389 |
r_angle_refined_deg | 3.306 |
r_scbond_it | 1.92 |
r_symmetry_vdw_refined | 0.397 |
r_nbd_refined | 0.394 |
r_nbtor_refined | 0.353 |
r_xyhbond_nbd_refined | 0.318 |
r_metal_ion_refined | 0.232 |
r_symmetry_hbond_refined | 0.179 |
r_chiral_restr | 0.138 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 219 |
Solvent Atoms | 28 |
Heterogen Atoms | 130 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
ADSC | data collection |
d*TREK | data reduction |
d*TREK | data scaling |
PHASER | phasing |