Joint X-ray/neutron room temperature structure of H/D-exchanged PLL lectin
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 5C9O | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | | 293 | 0.1 M sodium acetate, pD 4.2, 8 % (w/v) PEG 4000 dissolved in D2O |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 3.08 | 60.12 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 72.68 | α = 90 |
| b = 89.34 | β = 90 |
| c = 159.38 | 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 | 293 | CCD | ADSC QUANTUM 315r | | 2018-10-24 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 293 | IMAGE PLATE | LADI III | | 2018-09-03 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | ESRF BEAMLINE BM30A | 0.980 | ESRF | BM30A |
| 2 | NUCLEAR REACTOR | ILL BEAMLINE LADI III | 3.1-4.1 | 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 | 1.7 | 46 | 98.6 | 0.064 | | | | 1 | | 12.4 | 3.5 | | 56577 | | | 20.07 |
| 2 | 2.2 | 39 | 82.9 | 0.18 | | | | | | 2.8 | 2.8 | | 21855 | | | 20.07 |
| 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 | 1.7 | 2.02 | | 0.78 | | | | 0.63 | | | | |
| 2 | 2.2 | 2.32 | | 0.46 | | | | | | | | |
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 | 1.7 | 39.84 | | 1.35 | | 56568 | 2828 | 98.63 | | 0.1357 | 0.1346 | 0.13 | 0.1561 | 0.16 | | 31.76 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.2 | 38.97 | | | | 21821 | 1092 | 81.51 | | 0.2162 | 0.215 | | 0.2396 | | | 31.76 |
| X-RAY+NEUTRON | | | | | | | | | | | | | | | | | |
| 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 | 15.608 |
| f_angle_d | 1.3115 |
| f_chiral_restr | 0.0861 |
| f_bond_d | 0.0102 |
| f_plane_restr | 0.0065 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2750 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 340 |
| Heterogen Atoms | |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| SCALA | data scaling |
| PHENIX | phasing |
