3H30
Crystal structure of the catalytic subunit of human protein kinase CK2 with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | 1.5M ammonium sulfate, 0.2M tri-sodium citrate, 0.2M K/Na tartrate pH 5.6, the enzyme was preincubated with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.01 | 38.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 71.506 | α = 90 |
b = 71.506 | β = 90 |
c = 125.789 | γ = 90 |
Symmetry | |
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Space Group | P 43 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | CCD | MARMOSAIC 225 mm CCD | 2006-09-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X12 | 0.9 | EMBL/DESY, HAMBURG | X12 |
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 | 1.56 | 25 | 99.9 | 89590 | 89486 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.56 | 25 | 89590 | 87584 | 1860 | 99.91 | 0.15666 | 0.15666 | 0.15578 | 0.19811 | RANDOM | 23.844 |
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] | |
-1.02 | -1.02 | 2.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.235 |
r_dihedral_angle_3_deg | 13.674 |
r_dihedral_angle_4_deg | 13.665 |
r_dihedral_angle_1_deg | 5.708 |
r_scangle_it | 4.01 |
r_scbond_it | 3.211 |
r_mcangle_it | 2.495 |
r_mcbond_it | 1.948 |
r_angle_refined_deg | 1.189 |
r_mcbond_other | 0.92 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5667 |
Nucleic Acid Atoms | |
Solvent Atoms | 617 |
Heterogen Atoms | 92 |
Software
Software | |
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Software Name | Purpose |
MOLREP | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |