Structure of Gankyrin-S6ATPase photo-cross-linked site-specifically, and incoporated by genetic code expansion
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2DVW | PDB ENTRY 2DVW |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 298 | 31% polyethylene glycol 4000, 0.26M MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.27 | 45.8 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 103.164 | α = 90 |
| b = 103.164 | β = 90 |
| c = 154.993 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | H 3 |
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 | RAYONIX MX225HE | 2008-12-15 | M | SINGLE WAVELENGTH | ||||||
| 2 | 1 | x-ray | 100 | CCD | RAYONIX MX-225 | 2008-10-24 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | SPring-8 | BL41XU | |
| 2 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B2 | SPring-8 | BL26B2 | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.05 | 50 | 100 | 0.098 | 20.7 | 4.2 | 38604 | 26.5 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1,2 | 2.05 | 2.18 | 99.9 | 0.454 | 3.2 | 4.2 | 6083 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | 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 | THROUGHOUT | PDB ENTRY 2DVW | 2.05 | 42.93 | -3 | 38604 | 1914 | 100 | 0.171 | 0.171 | 0.16 | 0.229 | 0.22 | RANDOM | 37.4 | |||
| 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] | |
| 4.13 | 4.13 | -8.27 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| c_dihedral_angle_d | 21.9 |
| c_angle_deg | 2.8 |
| c_improper_angle_d | 1.78 |
| c_bond_d | 0.032 |
| c_bond_d_na | |
| c_bond_d_prot | |
| c_angle_d | |
| c_angle_d_na | |
| c_angle_d_prot | |
| c_angle_deg_na | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4668 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 327 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-2000 | data collection |
| MOLREP | phasing |
| CNS | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
