UDP-GlcNAc C4-epimerase mutant S121A/Y146F from Pseudomonas protegens in complex with UDP-GlcNAc
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1SB8 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, HANGING DROP | | 298 | 21% PEG 4000, 0.1 M sodium citrate pH 5.6, 0.2 M ammonium sulfate |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.85 | 56.79 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 124.195 | α = 90 |
| b = 75.487 | β = 90 |
| c = 79.271 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 21 21 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 | ADSC QUANTUM 315 | | 2013-07-30 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | NSLS BEAMLINE X29A | 1.075 | NSLS | X29A |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | fixed target |
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 | 2.1 | 50.03 | 100 | 0.122 | 23.6 | 7.6 | | 82655 | | | 26.33 |
| 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 | 2.1 | 2.18 | | | 0.722 | 3.6 | 12.5 | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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) | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1SB8 | 2.11 | 50.03 | 1.34 | 82655 | 3828 | 99.56 | 0.1579 | 0.1561 | 0.16 | 0.1945 | 0.19 | 31.65 |
| 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] |
|---|
| | | | | |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| f_dihedral_angle_d | 14.6306 |
| f_angle_d | 0.8634 |
| f_chiral_restr | 0.0486 |
| f_bond_d | 0.006 |
| f_plane_restr | 0.0048 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 4529 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 450 |
| Heterogen Atoms | 153 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| PHENIX | phasing |
