5F0A
CRYSTAL STRUCTURE OF PVX_084705 WITH BOUND 1-tert-butyl-3-(3-chlorophenoxy)-1H-pyrazolo[3,4-d]pyrimidin-4-amine INHIBITOR
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4MYI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 5% TACSIMATE, 0.1 M HEPES PH 7.0, 10% PEG 5000 MME, 16% SPERMIDINE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.94 | 68.76 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 192.172 | α = 90 |
b = 117.452 | β = 94.55 |
c = 67.699 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | CCD | MARMOSAIC 300 mm CCD | 2013-03-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 0.97945 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.6 | 50 | 99 | 0.08 | 9.2 | 3.5 | 45908 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.6 | 2.64 | 99.3 | 0.842 | 3.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | FOURIER SYNTHESIS | THROUGHOUT | 4MYI | 2.6 | 50 | 41768 | 2231 | 95.38 | 0.21026 | 0.20858 | 0.24238 | RANDOM | 71 |
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] | |
2.71 | 0.37 | -1.18 | -1.57 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.217 |
r_dihedral_angle_4_deg | 15.345 |
r_dihedral_angle_3_deg | 13.124 |
r_dihedral_angle_1_deg | 5.102 |
r_long_range_B_refined | 4.393 |
r_long_range_B_other | 4.339 |
r_mcangle_it | 1.904 |
r_mcangle_other | 1.904 |
r_scangle_other | 1.538 |
r_angle_refined_deg | 1.119 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6309 |
Nucleic Acid Atoms | |
Solvent Atoms | 178 |
Heterogen Atoms | 22 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |