Xylose Isomerase collected at 40C using serial fixed-target crystallography
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 6RNF | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | | 295 | (35% (w/v) PEG 3350, 200 mM LiSO4 and 10 mM Hepes/NaOH, pH 7.5) |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.78 | 55.79 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 94.2 | α = 90 |
| b = 103.05 | β = 90 |
| c = 99.25 | 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 | 313 | PIXEL | DECTRIS EIGER R 4M | | 2023-09-26 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) | 0.9763 | PETRA III, EMBL c/o DESY | P14 (MX2) |
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) | 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 | 1.7 | 71.49 | 98.89 | 0.9227 | 3.59 | 198.8 | | 53317 | | | 20.14 |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.7 | 1.761 | | | 0.3803 | | | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.7 | 71.49 | 1.33 | 53316 | 2606 | 99.89 | 0.1743 | 0.1727 | 0.174 | 0.2072 | 0.2085 | 23.47 |
| 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 | 12.7373 |
| f_angle_d | 0.6464 |
| f_chiral_restr | 0.0423 |
| f_plane_restr | 0.0071 |
| f_bond_d | 0.0039 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 3041 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 311 |
| Heterogen Atoms | 2 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| CrystFEL | data reduction |
| CrystFEL | data scaling |
| PHASER | phasing |
