5CVG
Crystal Structure of CK2alpha with a novel closed conformation of the aD loop
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5CVH | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 298 | 92mM Mes pH 6.5, 33% glycerol ethoxylate, 750mM ammonium acetate |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.78 | 31.05 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 57.587 | α = 90 |
| b = 44.086 | β = 110.38 |
| c = 62.039 | 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 PILATUS 6M | 2013-09-14 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9795 | Diamond | I04 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (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 | 1.25 | 35.13 | 90.8 | 0.042 | 0.042 | 0.027 | 0.998 | 14.8 | 3.2 | 73445 | 13.48 | ||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 1.25 | 1.254 | 48.3 | 0.446 | 0.446 | 0.271 | 0.829 | 2.1 | 2.4 | 9390 | |||||||||
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 | 5CVH | 1.25 | 35.13 | 73418 | 3686 | 90.82 | 0.154 | 0.1532 | 0.1698 | RANDOM | 18.75 | ||||||
| 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] | |
| -0.9824 | -1.9692 | 1.7528 | -0.7704 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| t_other_torsion | 15.06 |
| t_omega_torsion | 3.87 |
| t_angle_deg | 1.04 |
| t_bond_d | 0.011 |
| t_dihedral_angle_d | |
| t_trig_c_planes | |
| t_gen_planes | |
| t_it | |
| t_nbd | |
| t_improper_torsion | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2756 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 301 |
| Heterogen Atoms | 16 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| Aimless | data scaling |
| PHASER | phasing |
| BUSTER-TNT | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
