5Z3F
Glycosidase E335A in complex with glucose
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 298 | 0.2M Ammonium citrate tribasic (pH 6.8), 0.1M Sodium citrate (pH 5.5), 12% PEGmonomethyl ether 2000, 2mM isomaltose | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.79 | 55.99 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 104.83 | α = 90 |
| b = 104.83 | β = 90 |
| c = 89.45 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 4 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 PILATUS 2M | 2016-06-04 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NE3A | 1.0000 | Photon Factory | AR-NE3A |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.1 | 46.88 | 99.9 | 16.39 | 18.8 | 200183 | |||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
| 1 | 1.1 | 1.16 | |||||||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | THROUGHOUT | 1.1 | 46.88 | 190172 | 10011 | 99.93 | 0.10827 | 0.1076 | 0.12089 | RANDOM | 14.669 | ||||||||
| 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] | |
| 0.2 | 0.2 | -0.39 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.555 |
| r_sphericity_free | 23.817 |
| r_dihedral_angle_4_deg | 20.29 |
| r_sphericity_bonded | 13.977 |
| r_dihedral_angle_3_deg | 10.693 |
| r_rigid_bond_restr | 6.43 |
| r_long_range_B_refined | 5.715 |
| r_long_range_B_other | 5.715 |
| r_mcangle_other | 5.669 |
| r_mcangle_it | 5.639 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2858 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 430 |
| Heterogen Atoms | 43 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PHENIX | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
