3ISX
Crystal structure of Endoglucanase (TM1050) from THERMOTOGA MARITIMA at 1.40 A resolution
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 277 | 20.00% polyethylene glycol 3000, 0.1M citric acid pH 5.5, Additive: 0.001 M 1,10-phenanthroline, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.18 | 43.47 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 114.383 | α = 90 |
| b = 45.225 | β = 106.61 |
| c = 66.787 | 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 | CCD | MARMOSAIC 325 mm CCD | Flat collimating mirror, toroid focusing mirror | 2009-05-13 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | SSRL | BL9-2 | |
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 | 1.4 | 28.421 | 98.6 | 0.038 | 12.12 | 64412 | -3 | 15.065 | |||||||||||
| 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) | |||||||||||
| 1.4 | 1.45 | 98.6 | 0.467 | 1.9 | |||||||||||||||
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 | SAD | THROUGHOUT | 1.4 | 28.421 | 64410 | 3265 | 99.68 | 0.151 | 0.149 | 0.181 | RANDOM | 19.41 | |||||||
| 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] | |
| -0.36 | 0.04 | 0.13 | 0.25 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 28.754 |
| r_dihedral_angle_4_deg | 15.107 |
| r_dihedral_angle_3_deg | 11.518 |
| r_sphericity_free | 8.536 |
| r_dihedral_angle_1_deg | 5.625 |
| r_scangle_it | 5.302 |
| r_sphericity_bonded | 4.788 |
| r_scbond_it | 3.527 |
| r_mcangle_it | 2.637 |
| r_rigid_bond_restr | 1.729 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2639 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 374 |
| Heterogen Atoms | 12 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PHENIX | refinement |
| SHELX | phasing |
| MolProbity | model building |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| SHELXD | phasing |
| autoSHARP | phasing |
