Joint Xray/Neutron structure of Escherichia coli YajL at room temperature
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 2AB0 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | | 291 | 100 mM Tris pH=8.0, 250 mM MgCl2 and 20% PEG 4000 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.09 | 41.05 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 44.289 | α = 90 |
| b = 79.303 | β = 90 |
| c = 100.183 | 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 | x-ray | 293 | PIXEL | DECTRIS EIGER2 R 4M | | 2021-09-20 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 293 | SCINTILLATION | ORNL ANGER CAMERA | | 2021-09-07 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.542 | | |
| 2 | SPALLATION SOURCE | ORNL Spallation Neutron Source BEAMLINE MANDI | 2.00-4.16 | ORNL Spallation Neutron Source | MANDI |
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 | 1.65 | 100.18 | 99.7 | | | | | 0.995 | | 26.96 | 8.9 | | 43186 | | | 15.91 |
| 2 | 1.79 | 14.61 | 97.1 | | | | | 0.905 | | 12.7 | 6.9 | | 32647 | | | 15.91 |
| 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 | 1.65 | 1.71 | | | | | | 0.738 | | | | |
| 2 | 1.79 | 1.86 | | | | | | 0.604 | | | | |
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 | 1.65 | 25.56 | | 1.34 | | 43084 | 2215 | 99.64 | | 0.1385 | 0.1371 | 0.1368 | 0.1642 | 0.1634 | | 25.26 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.79 | 14.6 | | | | 32639 | | 96.73 | | | 0.1774 | | 0.2226 | | | |
| 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 | 16.752 |
| f_dihedral_angle_d | 16.752 |
| f_angle_d | 1.223 |
| f_angle_d | 1.223 |
| f_chiral_restr | 0.072 |
| f_chiral_restr | 0.072 |
| f_bond_d | 0.009 |
| f_bond_d | 0.009 |
| f_plane_restr | 0.007 |
| f_plane_restr | 0.007 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 2902 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 181 |
| Heterogen Atoms | |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
