6QE8
Crystal structure of Aspergillus niger GH11 endoxylanase XynA in complex with xylobiose epoxide activity based probe
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.1 M MES pH 5.5, 0.1 M NaCl, 1.8 M (NH4)2SO4 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.41 | 48.93 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 67.508 | α = 90 |
| b = 67.508 | β = 90 |
| c = 165.752 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 65 2 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 | 2018-02-05 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.976220 | Diamond | I03 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.79 | 47.77 | 100 | 0.033 | 12.8 | 23.3 | 21974 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.79 | 1.83 | 100 | 0.743 | 1.2 | 23.6 | |||||||||||||
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 | 2qz2 | 1.79 | 47.77 | 20827 | 1082 | 99.95 | 0.17901 | 0.17673 | 0.22259 | RANDOM | 31.718 | ||||||
| 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] | |
| 1.02 | 0.51 | 1.02 | -3.29 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.114 |
| r_dihedral_angle_4_deg | 14.362 |
| r_dihedral_angle_3_deg | 10.562 |
| r_dihedral_angle_1_deg | 8.943 |
| r_long_range_B_refined | 6.701 |
| r_long_range_B_other | 6.699 |
| r_scangle_other | 5.679 |
| r_scbond_it | 4.021 |
| r_scbond_other | 4.019 |
| r_mcangle_it | 3.3 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1401 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 160 |
| Heterogen Atoms | 71 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| xia2 | data reduction |
| xia2 | data scaling |
| REFMAC | phasing |
