6IK5
Crystal structure of tomato beta-galactosidase (TBG) 4 in complex with galactose
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.3 | 277 | 16% (w/v) PEG10000, 0.1M HEPES |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.18 | 43.55 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 92.136 | α = 90 |
| b = 95.335 | β = 90 |
| c = 158.327 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
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 | MARMOSAIC 225 mm CCD | 2016-09-19 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SPRING-8 BEAMLINE BL38B1 | 1.000000 | SPring-8 | BL38B1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (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 | 1.82 | 41.28 | 98.34 | 0.052 | 0.083 | 0.031 | 23.4 | 7.1 | 123244 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 1.82 | 1.885 | 95.47 | 0.615 | 0.782 | 0.297 | 2.68 | ||||||||||||
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 | 3W5G | 1.82 | 41.28 | 117286 | 6178 | 98.04 | 0.17344 | 0.17159 | 0.20867 | RANDOM | 24.951 | ||||||
| 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] | |
| -0.01 | 0.01 | -0.01 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.431 |
| r_dihedral_angle_4_deg | 18.633 |
| r_dihedral_angle_3_deg | 13.833 |
| r_long_range_B_refined | 9.104 |
| r_long_range_B_other | 9.09 |
| r_dihedral_angle_1_deg | 7.255 |
| r_scangle_other | 4.838 |
| r_mcangle_it | 4.117 |
| r_mcangle_other | 4.117 |
| r_scbond_it | 3.38 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 11062 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 885 |
| Heterogen Atoms | 108 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
| Coot | model building |
| PHENIX | refinement |
| REFMAC | refinement |
