Xylanase T6 (XT6) from Geobacillus Stearothermophilus in complex with xylohexaose
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1R86 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.7 | 293 | 30% PEG 4K, 0.01M ZnCl2, 0.1M MES buffer, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.33 | 63.09 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 121.8 | α = 90 |
| b = 61.67 | β = 119.38 |
| c = 89.35 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 2 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS HTC | 2013-09-10 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU | 1.54 | ||
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 | 1.8 | 43.07 | 89.4 | 4.6 | 45528 | 45528 | |||||||||||||
| 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 | 1.8 | 1.9 | 49 | ||||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | 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 | 1R86 | 1.8 | 43.07 | 45528 | 45528 | 2449 | 89.42 | 0.15341 | 0.15341 | 0.15126 | 0.17 | 0.19413 | 0.2 | RANDOM | 25.617 | ||
| 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] | |
| 0.88 | -0.2 | 0.4 | -0.71 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.803 |
| r_dihedral_angle_4_deg | 16.001 |
| r_dihedral_angle_3_deg | 14.615 |
| r_long_range_B_refined | 10.432 |
| r_long_range_B_other | 9.862 |
| r_dihedral_angle_1_deg | 6.779 |
| r_scangle_other | 5.476 |
| r_scbond_it | 3.663 |
| r_scbond_other | 3.633 |
| r_mcangle_other | 3.113 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3036 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 477 |
| Heterogen Atoms | 68 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-3000 | data collection |
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| REFMAC | phasing |
