6FT7
Crystal structure of CLK3 in complex with compound 8a
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2EU9 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7 | 277.15 | 21% PEG3350, 0.2 M sodium iodide, 0.1 M bis-tris-propane pH 7.0, 10% ethylene glycol |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.98 | 58.68 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 61.76 | α = 90 |
| b = 116.83 | β = 92.75 |
| c = 69.91 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 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 PILATUS3 6M | 2012-05-18 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | 0.97950 | Diamond | I02 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.02 | 59.95 | 96.7 | 0.091 | 8 | 3.7 | 62659 | 29 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.02 | 2.13 | 96 | 0.668 | 2.1 | ||||||||||||||
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2EU9 | 2.02 | 58.41 | 59444 | 3185 | 96.49 | 0.19395 | 0.1917 | 0.23523 | RANDOM | 42.83 | ||||||
| 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] | |
| -2.86 | -0.21 | 1.57 | 1.27 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_sphericity_bonded | 83.639 |
| r_sphericity_free | 47.092 |
| r_dihedral_angle_2_deg | 35.655 |
| r_dihedral_angle_4_deg | 18.739 |
| r_dihedral_angle_3_deg | 14.748 |
| r_dihedral_angle_1_deg | 5.978 |
| r_angle_refined_deg | 1.609 |
| r_angle_other_deg | 0.96 |
| r_chiral_restr | 0.098 |
| r_bond_refined_d | 0.015 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5800 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 485 |
| Heterogen Atoms | 100 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
