Neutron crystal structure of T4L M6AE
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 5VNQ | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | | 298 | ~2.0 M Na/K phosphate, pH 6-7, 250 mM NaCl |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.79 | 55.9 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 60.8 | α = 90 |
| b = 60.8 | β = 90 |
| c = 97.07 | γ = 120 |
| Symmetry |
|---|
| Space Group | P 32 2 1 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 298 | IMAGE PLATE | RIGAKU RAXIS IV++ | | 2017-08-01 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 298 | PIXEL | ORNL ANGER CAMERA | | 2017-08-01 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 | | |
| 2 | NUCLEAR REACTOR | ORNL Spallation Neutron Source BEAMLINE MANDI | 2.0-4.0 | 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 | 2.1 | 50 | 95.4 | 0.068 | | | | | | 8.9 | 2 | | 11921 | | | 31.1 |
| 2 | 1.9 | 15 | 91.2 | 0.1416 | | 0.1583 | | 0.989 | | 9.3 | 4.3 | | 15693 | | | 23.3 |
| 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 | 2.1 | 2.18 | | 0.457 | | | | | | 2 | | |
| 2 | 1.9 | 1.956 | | 0.2567 | | 0.3087 | 0.1656 | 0.138 | | 2.62 | | |
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 | 2.106 | 29.011 | | 1.34 | | 11921 | 581 | 95.48 | | 0.1864 | 0.1839 | 0.18 | 0.2354 | 0.24 | | 41.2012 |
| NEUTRON DIFFRACTION | | 1.889 | 14.505 | | | | 15693 | 772 | 91.46 | | 0.2184 | 0.2166 | | 0.254 | | | |
| 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] |
|---|
| | | | | |
| | | | | |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1305 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 87 |
| Heterogen Atoms | |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| Mantid | data reduction |
| LaueView | data scaling |
| PHASER | phasing |
