5HQ2
Structural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core particle
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 5.5 | 277 | 25 mM sodium acetate pH 5.5, 40 mM sodium citrate,1 mM DTT, 6% PEG2000-MME |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.1 | 60.37 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 100.729 | α = 90 |
b = 300.752 | β = 90 |
c = 182.09 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | ADSC QUANTUM 315 | 2013-07-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-E | 0.9792 | APS | 24-ID-E |
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 | 4.5 | 46.19 | 99.8 | 0.095 | 12.9 | 7.3 | 16854 | 16854 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 4.5 | 4.74 | 99.8 | 0.852 | 2.4 | 7.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 4.5 | 46 | 15908 | 845 | 99.32 | 0.34184 | 0.33904 | 0.3972 | RANDOM | 171.987 |
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] | |
11.93 | -7.31 | -4.62 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_long_range_B_other | 27.076 |
r_long_range_B_refined | 27.075 |
r_mcangle_it | 17.743 |
r_mcangle_other | 17.743 |
r_scangle_other | 16.727 |
r_scbond_it | 10.886 |
r_scbond_other | 10.885 |
r_mcbond_it | 9.967 |
r_mcbond_other | 9.951 |
r_dihedral_angle_1_deg | 6.318 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4767 |
Nucleic Acid Atoms | 2971 |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |