6W4L
The crystal structure of a single chain H2B-H2A histone chimera from Xenopus laevis
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1KX5 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 6.9 | 291 | 0.2M sodium thiocyanate, 20% PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.793 | α = 90 |
b = 44.679 | β = 117.27 |
c = 66.45 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 100 | CCD | MARMOSAIC 225 mm CCD | 2017-12-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.97931 | APS | 31-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.31 | 26.71 | 99.4 | 0.058 | 0.069 | 0.036 | 0.999 | 5.6 | 3.7 | 38073 | 13.7 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.31 | 1.39 | 99.8 | 0.892 | 1.052 | 0.55 | 0.619 | 3.6 |
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 | 1KX5 | 1.31 | 20 | 36283 | 1776 | 99.28 | 0.1712 | 0.1695 | 0.2063 | RANDOM | 20.418 |
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] | |
0.47 | -0.01 | -0.96 | 0.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.634 |
r_dihedral_angle_4_deg | 19.937 |
r_sphericity_free | 14.972 |
r_dihedral_angle_3_deg | 13.83 |
r_sphericity_bonded | 5.968 |
r_dihedral_angle_1_deg | 4.5 |
r_rigid_bond_restr | 1.788 |
r_angle_refined_deg | 1.541 |
r_angle_other_deg | 1.057 |
r_chiral_restr | 0.101 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1375 |
Nucleic Acid Atoms | |
Solvent Atoms | 43 |
Heterogen Atoms | 9 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
MOLREP | phasing |
Coot | model building |