5U5H
Crystal structure of EED in complex with 6-(2-fluoro-5-methoxybenzyl)-1-isopropyl-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine 6-(2-fluoro-5-methoxybenzyl)-1-isopropyl-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 291 | Crystals grown in a precipitant composed of 3-3.5 M sodium formate using the vapor diffusion method. Crystals grew in 3-5 days at 18 degree Celsius and harvested and soaked in defined drops consisting of 30 uL of precipitant with 1-2 mM of compound (typically solubilized in DMSO) for 24-48 h. Crystals were cryopreserved for data collection using a cryosolution consisting of 3.5 M sodium formate, 1-2 mM of compound, and 30% (v/v) glycerol. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 46.87 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.57 | α = 90 |
b = 60 | β = 103.86 |
c = 66.57 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | ADSC QUANTUM 315 | 2016-06-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.977408 | ALS | 5.0.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.8 | 64.63 | 97.2 | 6.8 | 3.2 | 34983 | 24.85 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.8 | 24.65 | 34960 | 1742 | 97.1 | 0.166 | 0.164 | 0.204 | RANDOM | 31.7 |
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] | |
-0.2689 | -4.4565 | 0.5519 | -0.283 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 17.3 |
t_omega_torsion | 4.07 |
t_angle_deg | 1.09 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2864 |
Nucleic Acid Atoms | |
Solvent Atoms | 338 |
Heterogen Atoms | 29 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
AMoRE | phasing |