Joint neutron and x-ray structure of alginate lyase PsAlg7C soaked with pentamannuronic acid
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 8C3X | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 293 | 30% PEG3350,0.1M Bis-Tris pH 5.5, 0.3M NaCl | |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 42.089 | α = 90 |
| b = 61.451 | β = 90 |
| c = 91.882 | 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 | neutron | 293 | SCINTILLATION | ORNL ANGER CAMERA | 2022-07-12 | L | LAUE | ||||||
| 2 | 2 | x-ray | 293 | PIXEL | DECTRIS EIGER R 4M | 2022-07-15 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SPALLATION SOURCE | ORNL Spallation Neutron Source BEAMLINE MANDI | 2-4 | ORNL Spallation Neutron Source | MANDI |
| 2 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 | 14.57 | 94.61 | 0.22 | 0.1 | 0.94 | 8.2 | 4.7 | 12772 | ||||||||||
| 2 | 2.1 | 27.42 | 100 | 0.12 | 0.05 | 0.99 | 12.4 | 6.3 | 14513 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
| 1 | 2.15 | 2.22 | 0.27 | 0.14 | 0.27 | 3.3 | |||||||||||||
| 2 | 2.1 | 2.16 | 0.66 | 0.29 | 0.8 | 4 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.15 | 14.57 | 12760 | 632 | 94.76 | 0.2371 | 0.2349 | 0.2767 | 19.74 | |||||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 2.1 | 27.41 | 14460 | 726 | 99.93 | 0.1303 | 0.1279 | 0.3531 | 0.1745 | 0.3576 | ||||||||
| 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_bond_d | 0.0129 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1768 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 124 |
| Heterogen Atoms | 61 |
