GH64 family beta-1,3-glucanase from Massilia violaceinigra
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | EVAPORATION | 7 | 298 | 2.8M NaAc |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.9 | 68.44 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 126.26 | α = 90 |
| b = 126.26 | β = 90 |
| c = 71.62 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 62 |
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 EIGER2 S 9M | 2024-12-21 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRF BEAMLINE BL02U1 | 0.979145 | SSRF | BL02U1 |
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 | 2.3 | 50 | 98 | 0.15 | 0.157 | 0.048 | 0.996 | 17 | 10.3 | 55571 | |||||||||
| 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 | 2.3 | 2.42 | 98.9 | 0.701 | 0.736 | 0.223 | 0.942 | 10.5 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | 2.3 | 47.36 | 27053 | 1425 | 98.07 | 0.16451 | 0.1637 | 0.172 | 0.17962 | 0.1868 | RANDOM | 27.583 | |||||
| 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] | |
| -0.3 | -0.15 | -0.3 | 0.99 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 19.448 |
| r_dihedral_angle_3_deg | 14.438 |
| r_long_range_B_other | 7.605 |
| r_long_range_B_refined | 7.591 |
| r_dihedral_angle_1_deg | 7.427 |
| r_scangle_other | 6.517 |
| r_mcangle_it | 4.831 |
| r_mcangle_other | 4.83 |
| r_scbond_it | 4.597 |
| r_scbond_other | 4.596 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2910 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 199 |
| Heterogen Atoms | 16 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| SCALA | data scaling |
| iMOSFLM | data reduction |
| MOLREP | phasing |
| PDB_EXTRACT | data extraction |
