4NK7
Crystal Structure of the D. melanogaster Plk4 cryptic polo box (CPB)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 298 | 100 mM HEPES-NaOH (pH 7.0), 2.5 M NaCl, 2 mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
6.64 | 81.48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 132.207 | α = 90 |
b = 132.207 | β = 90 |
c = 134.247 | γ = 120 |
Symmetry | |
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Space Group | P 64 2 2 |
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 | CCD | ADSC QUANTUM 315r | Toroidal focusing mirror | 2012-12-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | 0.9394 | ESRF | ID14-4 |
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 | 3.23 | 50 | 99.3 | 41.8 | 11619 | 11543 | 2 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 3.23 | 3.43 | 96.4 | 0.97 | 41.6 | 73134 |
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 (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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4G7N | 3.233 | 19.875 | 1.54 | 20915 | 11527 | 2076 | 99.5 | 0.2426 | 0.2403 | 0.2642 | RANDOM |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.83 |
f_angle_d | 1.059 |
f_chiral_restr | 0.061 |
f_plane_restr | 0.007 |
f_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1705 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DNA | data collection |
SOLVE | phasing |
PHENIX | refinement |
XDS | data reduction |
SCALA | data scaling |