2OSW
Endo-glycoceramidase II from Rhodococcus sp.
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 294 | 20% (w/v) PEG 3350; 0.175 M NaCl; 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.24 | 45.05 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 53.75 | α = 90 |
| b = 92.941 | β = 98.55 |
| c = 94.545 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 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 | MAR scanner 345 mm plate | 2005-11-11 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU | 1.5418 | ||
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 | 1.6 | 30.979 | 99.2 | 0.053 | 0.053 | 9.5 | 6.4 | 119859 | 19.957 | ||||||||||
| 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) | ||||||||||
| 1.6 | 1.69 | 98.2 | 0.335 | 0.335 | 2.2 | 6.4 | 17253 | ||||||||||||
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 | 1.6 | 29.57 | 119829 | 6081 | 99.1 | 0.183 | 0.181 | 0.204 | RANDOM | 13.701 | |||||||
| 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] | |
| 0.93 | -0.36 | 0.22 | -1.26 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.44 |
| r_dihedral_angle_3_deg | 11.774 |
| r_dihedral_angle_4_deg | 10.171 |
| r_dihedral_angle_1_deg | 5.717 |
| r_scangle_it | 1.659 |
| r_angle_refined_deg | 1.059 |
| r_scbond_it | 1.057 |
| r_angle_other_deg | 0.846 |
| r_mcangle_it | 0.747 |
| r_mcbond_it | 0.413 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6877 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 880 |
| Heterogen Atoms | 20 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SCALA | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| MAR345 | data collection |
| MOSFLM | data reduction |
| CCP4 | data scaling |
| SOLVE | phasing |
