5KH7
Crystal structure of fragment (3-[6-Oxo-3-(3-pyridinyl)-1(6H)-pyridazinyl]propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3C5K | pdbid 3C5K |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 291 | 2M Na-formate, 0.2M Na-acetate pH4.6, 5% ethylene glycol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.719 | α = 90 |
b = 43.776 | β = 90 |
c = 55.924 | γ = 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 | RIGAKU SATURN A200 | 2016-05-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E SUPERBRIGHT | 1.54178 |
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 | 1.6 | 34.47 | 99.9 | 0.03 | 0.033 | 0.012 | 1 | 43.5 | 6.7 | 13752 |
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 | 1.6 | 1.63 | 99.6 | 0.093 | 0.101 | 0.039 | 0.995 | 18.2 | 6.4 | 678 |
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 | THROUGHOUT | pdbid 3C5K | 1.7 | 34.47 | 10932 | 544 | 99.92 | 0.1479 | 0.1461 | 0.1827 | RANDOM | 9.628 |
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] | |
-0.01 | 0.49 | -0.48 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.966 |
r_dihedral_angle_4_deg | 15.452 |
r_dihedral_angle_3_deg | 11.206 |
r_dihedral_angle_1_deg | 6.388 |
r_angle_refined_deg | 1.489 |
r_mcangle_it | 1.237 |
r_angle_other_deg | 1.068 |
r_mcbond_it | 0.74 |
r_mcbond_other | 0.74 |
r_chiral_restr | 0.111 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 779 |
Nucleic Acid Atoms | |
Solvent Atoms | 117 |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |