6GZD
Crystal structure of Human CSNK1A1 with A86
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5FQD |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 277.15 | CSNK1A1 at a concentration of 5.8 mg/ml (50 mM Tris-HCl, 300 mM NaCl, 0.25 mM TCEP, pH 8.0) was pre-incubated with 0.7 mM (4.7-fold molar excess) of Mg2+-ATP (120 mM in UPW) for 1 h. 0.1 uL of the protein solution was then mixed with 0.1 uL of reservoir solution (0.10 M MES/NaOH pH 6.8, 10.0% 2-propanol, 26.0% PEG400) and equilibrated at 4 C over 0.06mL of reservoir solution. Well diffracting crystals appeared within 4 days and grew to full size over 23 days. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.02 | 59.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 113.383 | α = 90 |
b = 113.383 | β = 90 |
c = 80.878 | γ = 90 |
Symmetry | |
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Space Group | I 41 |
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 | 100.5 | PIXEL | DECTRIS PILATUS3 2M | 2017-06-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-1 | 0.966 | ESRF | MASSIF-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim 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 | 2.28 | 29.31 | 98.1 | 0.07 | 13.3 | 4 | 22991 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.28 | 2.4 | 0.56 |
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 | 5FQD | 2.28 | 29.31 | 21917 | 1071 | 98.01 | 0.17709 | 0.17496 | 0.22117 | RANDOM | 58.303 |
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] | |
-0.21 | -0.21 | 0.42 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.433 |
r_dihedral_angle_3_deg | 13.346 |
r_dihedral_angle_4_deg | 11.595 |
r_long_range_B_refined | 9.954 |
r_long_range_B_other | 9.949 |
r_scangle_other | 7.515 |
r_mcangle_it | 6.226 |
r_mcangle_other | 6.224 |
r_dihedral_angle_1_deg | 5.586 |
r_scbond_it | 5.056 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2456 |
Nucleic Acid Atoms | |
Solvent Atoms | 190 |
Heterogen Atoms | 141 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALA | data scaling |
REFMAC | phasing |
MOSFLM | data reduction |