5BSZ
X-ray structure of the sugar N-methyltransferase KedS8 from Streptoalloteichus sp ATCC 53650
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 3BXO | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 277 | 28-33% MPD, 2.5 mM SAH, 100 mM MOPS | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3 | 58.97 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 63.254 | α = 90 |
| b = 81.004 | β = 90 |
| c = 126.916 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 2 2 2 |
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 | Bruker Platinum 135 | 2015-05-02 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU RU200 | 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 | 2 | 30 | 97.6 | 0.045 | 0.045 | 14.3 | 3.4 | 21803 | 21803 | ||||||||||
| 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 | 2 | 2.1 | 94 | 0.143 | 4.2 | 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 | 3bxo | 2 | 28.71 | 20689 | 1114 | 97.09 | 0.17062 | 0.1678 | 0.22577 | RANDOM | 28.478 | ||||||
| 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] | |
| -1.2 | 0.31 | 0.89 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.47 |
| r_dihedral_angle_4_deg | 21.492 |
| r_dihedral_angle_3_deg | 14.893 |
| r_dihedral_angle_1_deg | 7.216 |
| r_angle_refined_deg | 1.95 |
| r_angle_other_deg | 0.841 |
| r_chiral_restr | 0.125 |
| r_bond_refined_d | 0.012 |
| r_gen_planes_refined | 0.009 |
| r_bond_other_d | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1885 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 162 |
| Heterogen Atoms | 59 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| SAINT | data reduction |
| SADABS | data scaling |
| PHASER | phasing |
