9CBJ
Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with p-Aminopropyl Phenylthioketone
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7U6A |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 10 mg/mL HDAC10 protein, 2 mM inhibitor, 0.2 M KH2PO4, 20% (w/v) PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.06 | 59.82 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.149 | α = 90 |
b = 81.149 | β = 90 |
c = 241.739 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | PIXEL | DECTRIS EIGER X 16M | Horizontal pre-focus bimorph mirror & KB bimorph mirrors | 2024-03-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 17-ID-2 | 0.98 | NSLS-II | 17-ID-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.48 | 33.74 | 100 | 0.135 | 0.045 | 0.998 | 9.2 | 9.9 | 33647 | 68.81 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.48 | 2.58 | 100 | 2.452 | 0.793 | 0.527 | 1 | 10.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | FREE R-VALUE | 2.48 | 33.74 | 1.33 | 33576 | 1996 | 99.95 | 0.2094 | 0.2076 | 0.2376 | 88.35 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.4647 |
f_angle_d | 0.5508 |
f_chiral_restr | 0.0415 |
f_plane_restr | 0.0046 |
f_bond_d | 0.0023 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4493 |
Nucleic Acid Atoms | |
Solvent Atoms | 28 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
autoPROC | data reduction |
Aimless | data scaling |
PHASER | phasing |