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 |
