4EZH
the crystal structure of KDM6B bound with H3K27me3 peptide
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8.2 | 293 | 11% methanol, 6% MPD, 5% PEG 4K, 5% Glycerol, HEPES 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.74 | 55.17 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 83.682 | ¦Á = 90 |
b = 102.413 | ¦Â = 90 |
c = 143.2 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 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 | 2011-06-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | APS | 24-ID-C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.5 | 40 | 99.9 | 0.111 | 0.072 | 7 | 41888 | 1.8 |
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 | 2.5 | 2.59 | 100 | 0.63 | 1.8 | 7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2.52 | 40 | 1.34 | 41888 | 41687 | 2105 | 98.7 | 0.215 | 0.213 | 0.254 |
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] | |
-9.5876 | 9.3638 | 0.2238 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.354 |
f_angle_d | 1.466 |
f_chiral_restr | 0.088 |
f_bond_d | 0.019 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7429 |
Nucleic Acid Atoms | |
Solvent Atoms | 82 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
PHASES | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |