4X9W
PLK-1 polo-box domain in complex with Bioactive Imidazolium-containing phosphopeptide macrocycle 4C
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3RQ7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 8 | 291 | Frozen stocks of protein at 37 mg/mL in 10 mM TRIS pH8, 0.5 M NaCl, 10 mM DTT were thawed and diluted to 10 mg/ml with the same buffer. Complexes with each of three macrocycle compounds (3b, 3c and 4b) were prepared by adding 100 mM stocks of the macrocycle in DMSO directly to the diluted protein to achieve a final concentration of 1 mM. Crystals were grown by hanging drop vapor diffusion, with drops made by mixing equal volumes of protein-macrocycle complex and well solution containing 2-6% PEG-3350. Crystals were cryo-protected by quickly dipping in a solution of 37.5% ethylene glycol in well solution and frozen in liquid nitrogen. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.92 | 36.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 36.052 | α = 90 |
b = 51.525 | β = 100.55 |
c = 57.449 | 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 | PIXEL | PSI PILATUS 6M | 2013-11-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.97950 | APS | 24-ID-C |
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) | 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 | 1.798 | 100 | 95.7 | 0.067 | 0.073 | 0.028 | 7 | 6.3 | 18528 | 27.05 |
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 | 1.798 | 1.83 | 80.2 | 0.301 | 0.329 | 0.132 | 0.965 | 5.4 | 753 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | FREE R-VALUE | 3RQ7 | 1.798 | 38.065 | 1.36 | 18493 | 1850 | 95.42 | 0.1987 | 0.1944 | 0.2388 | random |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.639 |
f_angle_d | 0.846 |
f_chiral_restr | 0.041 |
f_bond_d | 0.004 |
f_plane_restr | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1831 |
Nucleic Acid Atoms | |
Solvent Atoms | 73 |
Heterogen Atoms | 62 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data reduction |
PDB_EXTRACT | data extraction |
HKL-2000 | data scaling |
Coot | model building |
PHASER | phasing |