5FBB
S1 nuclease from Aspergillus oryzae in complex with phosphate and adenosine 5'-monophosphate
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 291 | 0.05 M Calcium chloride, 0.1 M BIS-TRIS pH 6.5, 30% v/v Polyethylene glycol monomethyl ether 550 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.02 | 39.2 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 42.84 | α = 106.42 |
| b = 47.64 | β = 90.09 |
| c = 62.6 | γ = 106.25 |
| 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 | MARMOSAIC 225 mm CCD | 2013-12-04 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | 0.91841 | BESSY | 14.2 |
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 | 1.75 | 35.51 | 95.8 | 0.102 | 8.1 | 2.2 | 43898 | 9.9 | |||||||||||
| 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 | 1.75 | 1.78 | 94.7 | 0.594 | 2.6 | 2.2 | |||||||||||||
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | our previous model of S1 | 1.75 | 35.51 | 43897 | 2252 | 95.85 | 0.14601 | 0.14476 | 0.18815 | Random selection | 16.102 | ||||||
| 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] | |
| -0.23 | 0.45 | -0.06 | 1.32 | 0.1 | -1.37 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.576 |
| r_dihedral_angle_4_deg | 14.587 |
| r_dihedral_angle_3_deg | 13.085 |
| r_dihedral_angle_1_deg | 5.751 |
| r_long_range_B_refined | 4.95 |
| r_long_range_B_other | 4.608 |
| r_scangle_other | 2.961 |
| r_scbond_it | 1.937 |
| r_scbond_other | 1.937 |
| r_mcangle_other | 1.917 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4098 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 439 |
| Heterogen Atoms | 168 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| iMOSFLM | data reduction |
| Aimless | data scaling |
| MOLREP | phasing |
| Coot | model building |
