Joint X-ray/neutron structure of protein kinase ck2 alpha subunit
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 3WAR | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION | 8.5 | 293 | 0.1M Tris-HCl, 0.85M ammonium sulfate, 5% acetonitrile, 2mM DTT |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2 | 38.45 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 58.604 | α = 90 |
| b = 45.442 | β = 111.83 |
| c = 63.612 | 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 | CCD | ADSC QUANTUM 315 | | 2014-02-04 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 100 | IMAGE PLATE | BIODIFF | | 2014-11-09 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 2 | NUCLEAR REACTOR | FRM II BEAMLINE BIODIFF | 2.668 | FRM II | BIODIFF |
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1.000 | Photon Factory | BL-5A |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 | 1.1 | 36 | 99.9 | 0.038 | | | | | | 21.3 | 5 | | 126644 | | | |
| 2 | 1.9 | 33.8 | 97 | 0.091 | | | | | | 8.5 | 2 | | 24039 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.1 | 1.14 | | 0.399 | | | | | | 4.3 | 3.4 | |
| 2 | 1.9 | 1.97 | | 0.451 | | | | | | 1.6 | 1.6 | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.1 | 36.01 | | 1.34 | | 126605 | 6332 | 99.6 | | 0.188 | 0.186 | 0.19 | 0.212 | 0.21 | | 32.7164 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.9 | 33.76 | | | | 24029 | 1203 | 96.9 | | 0.191 | 0.188 | | 0.247 | | | |
| 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] |
|---|
| | | | | |
| | | | | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| f_dihedral_angle_d | 16.356 |
| f_angle_d | 1.088 |
| f_chiral_restr | 0.092 |
| f_bond_d | 0.008 |
| f_plane_restr | 0.005 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2764 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 418 |
| Heterogen Atoms | 10 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| PHASER | phasing |
| DENZO | data reduction |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
