Crystal Structure of the alpha-L-arabinofuranosidase UmAbf62A from Ustilago maidys
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5 | 285 | 20% (w/v) PEG 3350, 0.2 M Sodium phosphate, 0.05 M Na Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 285.0K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 1.83 | 32.88 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 60.28 | α = 90 |
| b = 65.9 | β = 90 |
| c = 68.37 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 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 | OXFORD ONYX CCD | 2011-07-20 | M | SINGLE WAVELENGTH | ||||||
| 2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315r | 2011-06-22 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | 0.8266 | SOLEIL | PROXIMA 1 |
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 | ||||||||
| 1,2 | 1 | 37.3 | 99.4 | 0.098 | 10 | 5.5 | 146472 | 145655 | 1 | -3 | 15 | ||||||||
| 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) | |||||||||||
| 1,2 | 1 | 1.03 | 95.4 | 0.642 | 1.96 | 4 | 10217 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | SAD | THROUGHOUT | 1 | 37.3 | -3 | 138370 | 7283 | 99.45 | 0.11496 | 0.11369 | 0.1142 | 0.13946 | 0.1399 | RANDOM | 9.027 | ||||
| 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] | |
| 0.02 | -0.01 | -0.01 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_sphericity_free | 44.485 |
| r_dihedral_angle_2_deg | 31.744 |
| r_dihedral_angle_4_deg | 24.21 |
| r_sphericity_bonded | 12.21 |
| r_dihedral_angle_3_deg | 10.427 |
| r_dihedral_angle_1_deg | 8.069 |
| r_rigid_bond_restr | 7.323 |
| r_long_range_B_refined | 5.505 |
| r_long_range_B_other | 3.835 |
| r_scangle_other | 3.002 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2425 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 478 |
| Heterogen Atoms | 40 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| XDS | data scaling |
| SHELX | model building |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| SHELX | phasing |
