X-ray structure of glucuronoxylan-xylanohydrolase (Xyn30A) from Clostridium thermocellum at 1.77 A resolution
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4CKQ | PDB ENTRY 4CKQ |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 8.5 | 0.1 M TRIS-HCL 8.5, 8 % PEG 8000 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.48 | 50.49 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 46.62 | α = 65.16 |
| b = 50.33 | β = 67.56 |
| c = 58.71 | γ = 76.99 |
| Symmetry | |
|---|---|
| Space Group | P 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 | CCD | ADSC QUANTUM 315r | KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL | 2014-03-13 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | 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 | 1.77 | 45.53 | 93.4 | 0.13 | 14.15 | 4.1 | 40534 | 1.91 | |||||||||||
| 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 | 1.77 | 1.84 | 79.5 | 0.95 | 1.91 | 4 | |||||||||||||
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 4CKQ | 1.77 | 45.53 | 38598 | 1937 | 93.44 | 0.208 | 0.207 | 0.2138 | 0.237 | 0.246 | RANDOM | 21.07 | ||||
| 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 | 0.65 | 0.32 | -0.26 | 0.3 | ||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 41.456 |
| r_dihedral_angle_4_deg | 23.536 |
| r_dihedral_angle_3_deg | 12.158 |
| r_dihedral_angle_1_deg | 7.325 |
| r_angle_refined_deg | 1.838 |
| r_angle_other_deg | 0.898 |
| r_mcbond_it | 0.743 |
| r_mcbond_other | 0.743 |
| r_chiral_restr | 0.121 |
| r_bond_refined_d | 0.019 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3128 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 229 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PHASER | phasing |
