3EYP
Crystal structure of putative alpha-L-fucosidase from Bacteroides thetaiotaomicron
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 7 | 294 | 1.8M ammonium tri-citrate pH 7.0, Vapor diffusion, temperature 294K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.8 | 56.03 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 120.709 | α = 90 |
| b = 125.193 | β = 90 |
| c = 158.207 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 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 | MAR CCD 165 mm | 2008-10-15 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.97958 | APS | 31-ID |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.9 | 98.173 | 100 | 0.11 | 0.11 | 10 | 10.2 | 94178 | 94178 | 32.8 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 1.9 | 2 | 100 | 0.639 | 0.639 | 2.1 | 10.1 | 13620 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | SAD | THROUGHOUT | 1.9 | 20 | 94100 | 94091 | 4717 | 99.99 | 0.211 | 0.208 | 0.252 | RANDOM | 46.17 | ||||||
| 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] | |
| -1.83 | -0.6 | 2.43 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.594 |
| r_dihedral_angle_4_deg | 18.982 |
| r_dihedral_angle_3_deg | 15.212 |
| r_dihedral_angle_1_deg | 6.222 |
| r_scangle_it | 3.878 |
| r_scbond_it | 2.579 |
| r_angle_other_deg | 1.826 |
| r_angle_refined_deg | 1.613 |
| r_mcangle_it | 1.491 |
| r_mcbond_it | 0.901 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 7302 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 638 |
| Heterogen Atoms | 48 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SCALA | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| MAR345 | data collection |
| MOSFLM | data reduction |
| SHELXCD | phasing |
| SHELXE | model building |
