2HRI
A parallel stranded human telomeric quadruplex in complex with the porphyrin TMPyP4
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2A5R | PDB ENTRY 2A5R |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 6.5 | 285 | 500 mM ammonium sulphate, 80 mM lithium sulphate, 80 mM sodium chloride, 80 mM potassium chloride, 20mM potassium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 285K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.47 | 50.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 37.29 | α = 90 |
b = 61.99 | β = 90 |
c = 61.4 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | osmic mirrors | 2006-06-07 | 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 | 2.09 | 28.35 | 99.9 | 0.043 | 18.2 | 5.07 | 4443 | 4443 | 45 |
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 | 2.09 | 2.16 | 99.5 | 0.201 | 6.5 | 4.9 | 433 |
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 2A5R | 2.09 | 28.35 | 4239 | 4239 | 204 | 99.82 | 0.20062 | 0.20062 | 0.19829 | 0.24833 | RANDOM | 24.671 |
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] | |
-2.19 | 2.06 | 0.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_it | 2.577 |
r_angle_refined_deg | 2.16 |
r_scbond_it | 1.874 |
r_nbd_refined | 0.322 |
r_nbtor_refined | 0.308 |
r_symmetry_hbond_refined | 0.262 |
r_symmetry_vdw_refined | 0.249 |
r_xyhbond_nbd_refined | 0.173 |
r_metal_ion_refined | 0.107 |
r_chiral_restr | 0.092 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 462 |
Solvent Atoms | 46 |
Heterogen Atoms | 107 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |
PHASER | phasing |