Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with allosteric ligand FGC3330
Serial Crystallography (SX)
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 293 | 0.1 M bis-tris pH 5.5
23-26% (v/v) PEG 3350
0.2 M ammonia sulphate |
Crystal Properties |
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Matthews coefficient | Solvent content |
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3.09 | 60.17 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 126.645 | α = 90 |
b = 126.645 | β = 90 |
c = 124.25 | γ = 90 |
Symmetry |
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Space Group | P 43 21 2 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | | 2023-05-06 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | SYNCHROTRON | SLS BEAMLINE X06SA | 1.000030 | SLS | X06SA |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | | fixed target |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 |
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1 | 2.65 | 44.82 | 99.9 | 0.998 | 10.2 | 13.2 | | 30001 | | | |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 2.65 | 2.78 | | | 0.761 | | | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.65 | 44.82 | 28464 | 1480 | 99.93 | 0.22848 | 0.22642 | 0.26864 | RANDOM | 71.729 |
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] |
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3.99 | | | 3.99 | | -7.98 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_3_deg | 17.075 |
r_dihedral_angle_2_deg | 11.976 |
r_long_range_B_refined | 8.617 |
r_long_range_B_other | 8.617 |
r_dihedral_angle_1_deg | 6.85 |
r_scangle_other | 6.653 |
r_mcangle_it | 5.641 |
r_mcangle_other | 5.64 |
r_scbond_it | 4.506 |
r_scbond_other | 4.469 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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r_dihedral_angle_3_deg | 17.075 |
r_dihedral_angle_2_deg | 11.976 |
r_long_range_B_refined | 8.617 |
r_long_range_B_other | 8.617 |
r_dihedral_angle_1_deg | 6.85 |
r_scangle_other | 6.653 |
r_mcangle_it | 5.641 |
r_mcangle_other | 5.64 |
r_scbond_it | 4.506 |
r_scbond_other | 4.469 |
r_mcbond_it | 3.762 |
r_mcbond_other | 3.759 |
r_angle_refined_deg | 1.447 |
r_angle_other_deg | 0.55 |
r_chiral_restr | 0.082 |
r_bond_refined_d | 0.006 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.001 |
r_gen_planes_other | 0.001 |
r_dihedral_angle_4_deg | |
r_nbd_refined | |
r_nbd_other | |
r_nbtor_refined | |
r_nbtor_other | |
r_xyhbond_nbd_refined | |
r_xyhbond_nbd_other | |
r_metal_ion_refined | |
r_metal_ion_other | |
r_symmetry_vdw_refined | |
r_symmetry_vdw_other | |
r_symmetry_hbond_refined | |
r_symmetry_hbond_other | |
r_symmetry_metal_ion_refined | |
r_symmetry_metal_ion_other | |
r_scangle_it | |
r_rigid_bond_restr | |
r_sphericity_free | |
r_sphericity_bonded | |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 5343 |
Nucleic Acid Atoms | |
Solvent Atoms | 20 |
Heterogen Atoms | 167 |
Software
Software |
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Software Name | Purpose |
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REFMAC | refinement |
Aimless | data scaling |
XDS | data reduction |
MOLREP | phasing |