4YSM
Calcium-Dependent Protein Kinase from Eimeria tenella
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 298 | protein buffer: 25 mM HEPES pH 7.0, 5% glycerol, 500 mM NaCl, 2 mM DTT, 175 uM EtCDPK1; crystallization buffer: 100 mM BIS/TRIS pH 6.5, 23% PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.55 | 51.72 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.669 | α = 90 |
b = 109.556 | β = 92.17 |
c = 77.729 | 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 | 2014-11-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.97945 | SSRL | BL11-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | 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 | 3.19 | 38.84 | 98.8 | 0.497 | 0.203 | 0.976 | 5.6 | 6.9 | 18399 | 78 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 3.19 | 3.41 | 97.9 | 2.994 | 1.245 | 0.254 | 1 | 6.7 | 3280 |
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 3q5i | 3.19 | 38.84 | 17298 | 910 | 97.71 | 0.2311 | 0.2284 | 0.2804 | RANDOM | 73.509 |
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] | |
0.64 | 1.77 | 3.89 | -4.65 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.66 |
r_dihedral_angle_3_deg | 21.121 |
r_dihedral_angle_4_deg | 16.835 |
r_dihedral_angle_1_deg | 5.772 |
r_mcangle_it | 4.37 |
r_mcbond_it | 2.538 |
r_mcbond_other | 2.537 |
r_angle_refined_deg | 1.445 |
r_angle_other_deg | 0.993 |
r_chiral_restr | 0.078 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7518 |
Nucleic Acid Atoms | |
Solvent Atoms | 2 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |