Neutron crystal structure of human macrophage migration inhibitory factor
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 7XTX | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | | 283 | 0.49 M Monosodium phosphate, 0.91 M Dipotassium phosphate |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 3.83 | 67.9 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 96.534 | α = 90 |
| b = 96.534 | β = 90 |
| c = 105.596 | γ = 120 |
| Symmetry |
|---|
| Space Group | P 31 2 1 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | neutron | 293 | DIFFRACTOMETER | iBIX | The used detector is described in the paper (https://iopscience.iop.org/article/10.1088/1742-6596/528/1/012042/pdf). | 2020-06-24 | L | LAUE |
| 2 | 1 | x-ray | 293 | PIXEL | DECTRIS PILATUS3 6M | | 2020-10-25 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SPALLATION SOURCE | J-PARC MLF BEAMLINE BL-03 | 3.05-5.47 | JPARC MLF | BL-03 |
| 2 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1 | Photon Factory | BL-5A |
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 |
|---|
| 2 | 1.6 | 48.27 | 99.9 | | | | | 0.996 | | 14.7 | 10 | | 75394 | | | 20.95 |
| 1 | 2 | 20 | 99.4 | | | | | 0.984 | | 7.9 | 6.6 | | 38853 | | | |
| 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) |
|---|
| 2 | 1.6 | 1.63 | | | | | | 0.923 | | | | |
| 1 | 2 | 2.11 | | | | | | 0.431 | | | | |
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 | 1.6 | 44.64 | | 1.93 | | 75322 | 3993 | 100 | | 0.1547 | 0.1539 | 0.15 | 0.1692 | 0.17 | | 29.16 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2 | 20 | | | | 38853 | | 99.4 | | | 0.18 | | 0.2 | | | |
| 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 | 19.1828 |
| f_angle_d | 1.5558 |
| f_chiral_restr | 0.113 |
| f_bond_d | 0.041 |
| f_plane_restr | 0.0074 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2579 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 215 |
| Heterogen Atoms | |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| SCALA | data scaling |
| MOLREP | phasing |
| PDB_EXTRACT | data extraction |
