6ZRB
Crystal structure of SMYD3 conjugate with piperidine-based covalent inhibitor EM127
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.25 | 298 | Protein was pre-incubated with the covalent inhibitor, 7 mg/mL and 0.4 mM, respectively, for 8 h at RT. Crystallization was performed in 2 uL hanging drops, 1:1 protein to reservoir ratio, reservoir: 16% PEG3350, 100 mM Tris (pH 8.25), 100 mM Mg(OAc)2). Protein crystals were cryoprotected in 20% PEG3350, 100 mM Tris (pH 8.25), 100 mM Mg(OAc)2, 10% DMSO and 10% glycerol. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.21 | 44.33 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.935 | α = 90 |
b = 65.989 | β = 90 |
c = 107.318 | 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 | PIXEL | DECTRIS EIGER X 16M | 2019-04-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX IV BEAMLINE BioMAX | 0.918 | MAX IV | BioMAX |
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 | 1.55 | 107.32 | 98.7 | 0.052 | 0.057 | 0.025 | 0.999 | 16.4 | 5 | 62691 |
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 | 1.55 | 1.58 | 86.6 | 0.45 | 0.532 | 0.277 | 0.789 | 2.3 | 3.3 |
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 | 6Z2R | 1.55 | 56.28 | 59518 | 3106 | 98.58 | 0.1664 | 0.1654 | 0.1845 | RANDOM | 21.465 |
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] | |
1.14 | -0.39 | -0.75 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.973 |
r_dihedral_angle_4_deg | 15.346 |
r_dihedral_angle_3_deg | 13.64 |
r_dihedral_angle_1_deg | 6.093 |
r_angle_other_deg | 2.316 |
r_mcangle_it | 2.206 |
r_angle_refined_deg | 1.517 |
r_mcbond_other | 1.402 |
r_mcbond_it | 1.401 |
r_chiral_restr | 0.083 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3402 |
Nucleic Acid Atoms | |
Solvent Atoms | 412 |
Heterogen Atoms | 54 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |