7XVM
Crystal Structure of Nucleosome-H5 Linker Histone Assembly (sticky-169a DNA fragment)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 291 | 40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.42 | 49.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 105.16 | α = 90 |
b = 103.758 | β = 100.97 |
c = 212.955 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 | 98.15 | PIXEL | DECTRIS PILATUS 2M-F | 2017-09-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 1 | SLS | X06DA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | 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 | 2.84 | 48.03 | 98.8 | 0.999 | 13.7 | 6.6 | 105157 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.84 | 2.99 | 92.4 | 0.421 | 1 | 6.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | 3UT9, 4QLC | 2.84 | 48.03 | 103041 | 2096 | 98.83 | 0.20155 | 0.20039 | 0.25898 | RANDOM | 116.381 |
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] | |
-2.09 | 0.3 | 4.51 | -2.36 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.921 |
r_dihedral_angle_3_deg | 19.151 |
r_dihedral_angle_4_deg | 17.954 |
r_long_range_B_refined | 14.31 |
r_long_range_B_other | 14.31 |
r_scangle_other | 10.995 |
r_mcangle_it | 9.046 |
r_mcangle_other | 9.045 |
r_scbond_it | 7.103 |
r_scbond_other | 7.103 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13813 |
Nucleic Acid Atoms | 13846 |
Solvent Atoms | 11 |
Heterogen Atoms | 23 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |