Structure of the D10N mutant of beta-phosphoglucomutase from Lactococcus lactis trapped with native reaction intermediate beta-glucose 1,6-bisphosphate to 2.2A resolution.
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2WF5 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.2 | 291 | 24-34% PEG 4000 200mM Tris pH 7.5 200mM sodium acetate harvested after 1 week |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.19 | 43.85 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 36.81 | α = 90 |
| b = 54.94 | β = 90 |
| c = 103.34 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 6M | 2016-07-10 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.97950 | Diamond | I04 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | 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 | 2.15 | 48.51 | 100 | 0.339 | 0.148 | 0.98 | 5.3 | 6.2 | 11990 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 2.15 | 2.19 | 100 | 1.683 | 0.721 | 0.391 | 1.2 | 6.4 | |||||||||||
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 | 2WF5 | 2.15 | 48.51 | 11376 | 571 | 99.88 | 0.2235 | 0.2201 | 0.23 | 0.29234 | 0.3 | RANDOM | 31.793 | ||||
| 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] | |
| -1.75 | -0.87 | 2.62 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 43.342 |
| r_dihedral_angle_3_deg | 15.83 |
| r_dihedral_angle_4_deg | 11.012 |
| r_dihedral_angle_1_deg | 6.524 |
| r_long_range_B_refined | 4.902 |
| r_long_range_B_other | 4.901 |
| r_scangle_other | 3.546 |
| r_mcangle_other | 2.782 |
| r_mcangle_it | 2.781 |
| r_scbond_it | 2.186 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1680 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 84 |
| Heterogen Atoms | 26 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| Coot | model building |
| XDS | data reduction |
| xia2 | data scaling |
