Joint X-ray/neutron room temperature structure of perdeuterated LecB lectin in complex with perdeuterated fucose
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1GZT | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | | 292 | 0.1 M Tris/DCl, pD 7.1, 20% (w/v) PEG 4000 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.26 | 45.5 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 52.9 | α = 90 |
| b = 73.87 | β = 94.58 |
| c = 55.003 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 1 21 1 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 293 | IMAGE PLATE | MAR scanner 345 mm plate | | 2020-09-16 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 293 | IMAGE PLATE | LADI III | | 2020-08-18 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SEALED TUBE | Xenocs GeniX 3D Cu HF | 1.5418 | | |
| 2 | NUCLEAR REACTOR | ILL BEAMLINE LADI III | 2.8-3.8 | ILL | LADI III |
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 | 1.85 | 33 | 96.6 | 0.097 | | | | 1 | | 11.3 | 7 | | 34855 | | | 12.85 |
| 2 | 1.9 | 43 | 73.8 | | | | 10.9 | | | 5.5 | 3.7 | | 24478 | | | 12.85 |
| 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 | 1.85 | 1.89 | | | | | | 0.85 | | | | |
| 2 | 1.9 | 2.08 | | | | | 17 | | | | | |
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 |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.85 | 27.41 | | 1.36 | | 34734 | 1736 | 96.22 | | 0.1061 | 0.1042 | 0.1 | 0.1419 | 0.14 | | 21.52 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.9 | 42.92 | | | | 24283 | 1195 | 72.84 | | 0.1941 | 0.1914 | | 0.2461 | | | |
| 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 | 17.8892 |
| f_dihedral_angle_d | 17.8892 |
| f_angle_d | 1.2693 |
| f_angle_d | 1.2693 |
| f_chiral_restr | 0.074 |
| f_chiral_restr | 0.074 |
| f_bond_d | 0.0101 |
| f_bond_d | 0.0101 |
| f_plane_restr | 0.0068 |
| f_plane_restr | 0.0068 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 3308 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 364 |
| Heterogen Atoms | 57 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| iMOSFLM | data reduction |
| Coot | model building |
| SCALA | data scaling |
| PHASER | phasing |
