3GDA
Crystal study of d(CACGCG).d(CGCGTG) grwon in presence of stannous chloride
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.99 | 293 | Sodium cacodylate 50mM, SnCl2 0.5mM, Spermine 10mM, Methyl pentane diol 33%, pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 17.552 | α = 90 |
b = 30.207 | β = 90 |
c = 43.682 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | MAR scanner 345 mm plate | mirrors | 2008-11-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.54 |
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 | 1.87 | 12 | 99.1 | 0.0579 | 0.0501 | 6.7 | 4.05 | 2132 | 2113 | 38.47 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.87 | 1.94 | 98.6 | 0.332 | 0.2838 | 1.1 | 4.18 | 206 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | Z-DNA FIBER MODEL BUILT WITH INSIGHT-II | 1.88 | 10.92 | 1999 | 1992 | 107 | 99.62 | 0.24219 | 0.241 | 0.26596 | RANDOM | 25.051 |
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] | |
0.09 | -0.11 | 0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scbond_it | 2.676 |
r_scangle_it | 2.675 |
r_angle_refined_deg | 2.015 |
r_nbtor_refined | 0.282 |
r_symmetry_vdw_refined | 0.277 |
r_symmetry_hbond_refined | 0.203 |
r_nbd_refined | 0.162 |
r_xyhbond_nbd_refined | 0.158 |
r_chiral_restr | 0.073 |
r_bond_refined_d | 0.011 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 240 |
Solvent Atoms | 19 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
AMoRE | phasing |
REFMAC | refinement |
AUTOMAR | data reduction |
SCALEPACK | data scaling |