6FJ9
Structure of Thaumatin collected from an in situ crystal on ID30B at 17.5 keV.
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 5A47 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 0.1M HEPES and 0.7 M potassium/sodium tartrate |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.93 | 58 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 58.57 | α = 90 |
| b = 58.57 | β = 90 |
| c = 151.544 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 293 | PIXEL | DECTRIS PILATUS3 6M | Be CRL (vertical focusing) and Rh stripe Elliptical mirror (horizontal focusing) | 2016-09-12 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID30B | 0.7085 | ESRF | ID30B |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.5 | 54.63 | 92.6 | 0.086 | 0.111 | 0.057 | 0.99 | 7.2 | 3.4 | 39794 | 12.4 | ||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 1.5 | 1.53 | 96.7 | 0.727 | 0.979 | 0.518 | 0.6 | 1.3 | 3.4 | ||||||||||
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 | 5a47 | 1.5 | 54.63 | 37747 | 1985 | 92.02 | 0.1382 | 0.13673 | 0.16678 | RANDOM | 19.775 | ||||||
| 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] | |
| 0.04 | 0.04 | -0.08 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 41.349 |
| r_sphericity_free | 22.123 |
| r_dihedral_angle_4_deg | 15.25 |
| r_dihedral_angle_3_deg | 11.987 |
| r_dihedral_angle_1_deg | 9.826 |
| r_sphericity_bonded | 8.756 |
| r_long_range_B_refined | 2.286 |
| r_long_range_B_other | 2.284 |
| r_rigid_bond_restr | 1.975 |
| r_scangle_other | 1.972 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1545 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 121 |
| Heterogen Atoms | 10 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MxCuBE | data collection |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
