3KAI
Structure-guided design of alpha-amino acid-derived Pin1 inhibitors
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1PIN | PDB ENTRY 1PIN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 277 | 2.2M Ammonium sulphate, 0.1M HEPES buffer, 1% PEG 400, 5mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.91 | 57.71 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.64 | α = 90 |
b = 68.64 | β = 90 |
c = 79.233 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | IMAGE PLATE | RIGAKU RAXIS IV++ | mirrors | 2007-08-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R | 1.5418 |
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 | 1.9 | 59.44 | 96.1 | 0.06 | 5.6 | 2.1 | 16782 | 16782 | 1 | 1 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
1.9 | 1.97 | 85.3 | 0.353 | 1.7 | 2.1 | 1010 |
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 | PDB ENTRY 1PIN | 1.9 | 29.7 | 15921 | 861 | 96.01 | 0.20802 | 0.20569 | 0.254 | RANDOM | 32.684 |
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] | |
0.68 | 0.34 | 0.68 | -1.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.732 |
r_dihedral_angle_4_deg | 23.699 |
r_dihedral_angle_3_deg | 15.041 |
r_dihedral_angle_1_deg | 7.197 |
r_scangle_it | 6.291 |
r_scbond_it | 3.858 |
r_mcangle_it | 2.401 |
r_angle_refined_deg | 2.12 |
r_mcbond_it | 1.326 |
r_chiral_restr | 0.152 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1162 |
Nucleic Acid Atoms | |
Solvent Atoms | 116 |
Heterogen Atoms | 49 |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
AMoRE | phasing |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |