2AVH
G4T3G4 dimeric quadruplex structure
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 284.15 | sodium iodide, sodium cacodylate, PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 284.15K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
1.83 | 32.14 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 29.932 | α = 90 |
b = 37.112 | β = 90 |
c = 43.653 | γ = 90 |
Symmetry | |
---|---|
Space Group | C 2 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 99 | CCD | ADSC QUANTUM 4 | 2004-11-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 0.9792 | ESRF | ID14-4 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.5 | 25 | 99 | 0.054 | 4066 | 4066 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1.5 | 1.54 | 96.127 | 98.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | GGGG(+U)TTGGGG chain A (P21) | 1.5 | 23.3 | 4065 | 4065 | 184 | 98.91 | 0.199 | 0.199 | 0.198 | 0.208 | RANDOM | 19.437 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.66 | 0.49 | 0.16 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_scangle_it | 1.517 |
r_angle_refined_deg | 1.15 |
r_scbond_it | 1.03 |
r_symmetry_vdw_refined | 0.375 |
r_nbd_refined | 0.31 |
r_nbtor_refined | 0.272 |
r_symmetry_hbond_refined | 0.125 |
r_xyhbond_nbd_refined | 0.11 |
r_symmetry_metal_ion_refined | 0.096 |
r_metal_ion_refined | 0.06 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 233 |
Solvent Atoms | 54 |
Heterogen Atoms | 4 |
Software
Software | |
---|---|
Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
EPMR | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |