Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Z-DNA (X-ray)
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION | 5.6 | 293 | 0.01M Magnesium Acetate
0.05M MES pH 5.6
2.5M Ammonium Sulfate, VAPOR DIFFUSION, temperature 293K |
Crystal Properties |
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Matthews coefficient | Solvent content |
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1.76 | 30.3 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 17.9 | α = 90 |
b = 30.59 | β = 90 |
c = 44.61 | γ = 90 |
Symmetry |
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Space Group | P 21 21 21 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 293 | CCD | RIGAKU SATURN 92 | | 2006-01-01 | M | SINGLE WAVELENGTH |
2 | 1 | 293 | AREA DETECTOR | | | 2006-01-01 |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | ROTATING ANODE | RIGAKU FR-E DW | 1.54 | | |
2 | NUCLEAR REACTOR | | 0.6-0.7 | | |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 |
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1 | 1.53 | 100 | 92.1 | | | | | | | | | 3696 | 3696 | | | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | 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 |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.53 | 100 | | | 3696 | 3696 | 178 | | | | 0.1937 | 0.2359 | random, throughout | |
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.4 | 100 | | | 4680 | 4680 | 240 | | | | 0.3007 | 0.3147 | random, throughout | |
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] |
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Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | |
Nucleic Acid Atoms | 240 |
Solvent Atoms | 41 |
Heterogen Atoms | |
Software
Software |
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Software Name | Purpose |
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CrystalClear | data collection |
PHASER | phasing |
nCNS-TINKER | refinement |
d*TREK | data reduction |
SCALA | data scaling |