460D
A "HYDRAT-ION SPINE" IN A B-DNA MINOR GROOVE
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.9 | 275 | SITTING DROPLETS CONTAINING 1.2 MM OLIGONUCLEOTIDE, 20 MM RB CACODYLATE PH 6.9, 25 MM MAGNESIUM ACETATE, 3.2 MM SPERMINE TETRACLORIDE AGAINST RESERVOIR OF 40% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 275K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.84 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 25.111 | α = 90 |
b = 39.731 | β = 90 |
c = 65.829 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 100 | CCD | MARRESEARCH | 1998-11-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 5ID-B | APS | 5ID-B |
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 | 1.2 | 20 | 97.3 | 0.068 | 5.8 | 20661 | 20661 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.24 | 93.3 | 0.115 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | 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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | 1.2 | 20 | 20661 | 20661 | 93.3 | 0.179 | 0.179 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_angle_d | 0.021 |
s_bond_d | 0.008 |
s_similar_dist | |
s_from_restr_planes | |
s_zero_chiral_vol | |
s_non_zero_chiral_vol | |
s_anti_bump_dis_restr | |
s_rigid_bond_adp_cmpnt | |
s_similar_adp_cmpnt | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 508 |
Solvent Atoms | 189 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
AMoRE | phasing |
SHELXL-97 | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |