4MBI
Discovery of Pyrazolo[1,5a]pyrimidine-based Pim1 Inhibitors
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.4 | 298 | 10.5% PEG 400, 0.05 M Tris-Cl pH 8.4, 0.3 M NaCl, 0.01 M DTT, 0.01M EDTA, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.29 | 62.66 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 97.877 | α = 90 |
b = 97.877 | β = 90 |
c = 80.625 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
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 | 200 | IMAGE PLATE | RIGAKU RAXIS IV++ | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
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 | 2.3 | 29.8 | 80.9 | 21340 | 17271 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | 2.3 | 29.77 | 15715 | 15715 | 1769 | 89.25 | 0.21484 | 0.21125 | 0.24564 | RANDOM | 30.024 |
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] | |
0.9 | 0.45 | 0.9 | -1.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.61 |
r_dihedral_angle_4_deg | 20.728 |
r_dihedral_angle_3_deg | 16.202 |
r_dihedral_angle_1_deg | 6.856 |
r_scangle_it | 3.128 |
r_scbond_it | 2.02 |
r_angle_refined_deg | 1.705 |
r_mcangle_it | 1.251 |
r_angle_other_deg | 0.96 |
r_mcbond_it | 0.687 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2230 |
Nucleic Acid Atoms | |
Solvent Atoms | 124 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
AMoRE | phasing |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |