6FJ6
Structure of Thaumatin collected at 100K on ID30B
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3E0A | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 0.1 M HEPES, 0.7 M sodium/potassium tartrate and 20% glycerol. |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.85 | 56.9 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 57.951 | α = 90 |
| b = 57.951 | β = 90 |
| c = 150.725 | 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 | 100 | PIXEL | DECTRIS PILATUS3 6M | Be CRL (vertical focusing) and Rh coating elliptical mirror (horizontal focusing) | 2017-06-15 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID30B | 0.9787 | 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 | 1.08 | 54.09 | 89.9 | 0.054 | 0.069 | 0.029 | 0.996 | 11.8 | 3.6 | 99222 | 11.6 | ||||||||
| 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 | 1.08 | 1.12 | 63.5 | 0.514 | 0.845 | 0.544 | 0.857 | 0.8 | 1.6 | ||||||||||
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 | 3e0a | 1.08 | 54.09 | 91794 | 4831 | 87.37 | 0.149 | 0.14808 | 0.16645 | RANDOM | 17.711 | ||||||
| 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] | |
| -0.5 | -0.5 | 1 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.201 |
| r_sphericity_free | 27.678 |
| r_dihedral_angle_4_deg | 17.695 |
| r_sphericity_bonded | 11.66 |
| r_dihedral_angle_3_deg | 10.88 |
| r_dihedral_angle_1_deg | 10.292 |
| r_long_range_B_refined | 3.11 |
| r_rigid_bond_restr | 3.079 |
| r_long_range_B_other | 2.898 |
| r_scangle_other | 2.735 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1547 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 171 |
| Heterogen Atoms | 34 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| MxCuBE | data collection |
| XDS | data reduction |
| pointless | data scaling |
| PHASER | phasing |
