Neutron crystal structure of wtT4LD
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 | 6 | 298 | ~2.0 M Na/K phosphate, pH 6-7, 250 mM NaCl |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.78 | 55.83 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 60.87 | α = 90 |
| b = 60.87 | β = 90 |
| c = 97 | 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 | IMAGE PLATE | 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 | 1.95 | 35 | 99.9 | 0.109 | | | | | | 16.7 | 5.8 | | 15677 | | | |
| 2 | 2.1 | 15 | 78.8 | 0.178 | | | | | | 6.5 | 3.3 | | 10071 | | | |
| 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 | 1.95 | 2.02 | | 0.462 | | | | | | 4.7 | | |
| 2 | 2.1 | 2.18 | | 0.2743 | | | | | | 2.68 | | |
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 | 1.951 | 35 | | 1.35 | | 15677 | 631 | 99.97 | | 0.1658 | 0.1641 | 0.17 | 0.1984 | 0.2 | | 30.583 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.101 | 14.457 | | | | 10071 | 501 | 80.14 | | 0.2204 | 0.2187 | | 0.251 | | | |
| 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 | 1309 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 91 |
| Heterogen Atoms | 1 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| Mantid | data reduction |
| LaueView | data scaling |
| PHASER | phasing |
