4D1J
The structure of the GH35 beta-galactosidase Bgl35A from Cellvibrio japonicas in complex with 1-Deoxygalactonojirimycin
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3U7V | PDB ENTRY 3U7V |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7 | 2.8 M SODIUM ACETATE PH 7.0 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.7 | 54.4 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 99.257 | α = 90 |
| b = 116.095 | β = 90.05 |
| c = 116.113 | γ = 90.04 |
| Symmetry | |
|---|---|
| Space Group | P 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 | PIXEL | DECTRIS PILATUS 6M | 2013-05-26 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | Diamond | I03 | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.8 | 50 | 97.1 | 0.05 | 9.8 | 2.2 | 466658 | -3.7 | 20.1 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.8 | 1.83 | 95.8 | 0.57 | 1.4 | 2.1 | |||||||||||||
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 | PDB ENTRY 3U7V | 1.8 | 116.11 | 443137 | 23426 | 97.08 | 0.17286 | 0.17169 | 0.19482 | RANDOM | 28.627 | ||||||
| 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] | |
| 1.4 | 0.13 | 0.64 | -0.35 | 0.21 | -1.05 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.442 |
| r_dihedral_angle_4_deg | 20.418 |
| r_dihedral_angle_3_deg | 13.394 |
| r_dihedral_angle_1_deg | 6.608 |
| r_scangle_it | 3.86 |
| r_mcangle_it | 2.814 |
| r_scbond_it | 2.537 |
| r_mcbond_it | 1.952 |
| r_mcbond_other | 1.952 |
| r_angle_refined_deg | 1.466 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 33387 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 4011 |
| Heterogen Atoms | 131 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
