Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) bound to compound 18 (CS587)
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2JC6 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 5.9 | 293 | 0,1M NaCit, pH 5.9 2,05M AmmSO4 0,1M Na/K tartrate |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 57.82 | α = 90 |
| b = 45.64 | β = 104.183 |
| c = 108.754 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 1 2 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2017-09-24 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.95372 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.48 | 55.45 | 98.7 | 0.026 | 0.999 | 14.8 | 6.3 | 44955 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 1.48 | 1.51 | 98.3 | 0.155 | 0.883 | 4.2 | 6.6 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 (All) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2jc6 | 1.484 | 55.448 | 44954 | 2291 | 98.465 | 0.137 | 0.1355 | 0.1363 | 0.1747 | 0.1736 | 17.818 | |||||
| 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] | |
| 0.727 | -0.17 | -0.188 | -0.402 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.006 |
| r_dihedral_angle_4_deg | 21.923 |
| r_dihedral_angle_3_deg | 11.751 |
| r_dihedral_angle_1_deg | 6.255 |
| r_lrange_it | 3.535 |
| r_lrange_other | 3.535 |
| r_scangle_it | 2.815 |
| r_scangle_other | 2.815 |
| r_mcangle_it | 2.324 |
| r_mcangle_other | 2.323 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2175 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 197 |
| Heterogen Atoms | 73 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| iMOSFLM | data reduction |
| Aimless | data scaling |
| MOLREP | phasing |
