7XX5
Crystal Structure of Nucleosome-H1.3 Linker Histone Assembly (sticky-169a DNA fragment)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 291 | 40-45mM CaCl2, 25mM KCl, 10mM Na-acetate (pH 4.5) | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.5 | 50.88 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 105.071 | α = 90 |
| b = 101.736 | β = 103.52 |
| c = 218.399 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 2015-09-22 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SLS BEAMLINE X06DA | 1 | SLS | X06DA |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 3.19 | 47.21 | 98.5 | 0.998 | 10.2 | 3.3 | 73544 | ||||||||||||
| 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 | 3.19 | 3.37 | 96.1 | 0.532 | 1.4 | 3.2 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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, 2LSO | 3.19 | 46.57 | 69849 | 3677 | 98.41 | 0.20573 | 0.20286 | 0.25943 | RANDOM | 123.138 | ||||||
| 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] | |
| -3.89 | -0.18 | -2.85 | 6.12 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.096 |
| r_dihedral_angle_3_deg | 18.683 |
| r_dihedral_angle_4_deg | 18.391 |
| r_long_range_B_refined | 13.035 |
| r_long_range_B_other | 13.035 |
| r_scangle_other | 9.626 |
| r_mcangle_other | 8.16 |
| r_mcangle_it | 8.159 |
| r_scbond_it | 6.086 |
| r_scbond_other | 6.086 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 12758 |
| Nucleic Acid Atoms | 13846 |
| Solvent Atoms | |
| Heterogen Atoms | 13 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
