Neutron crystal structure of Panus similis AA9A at room temperature
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 5N04 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 3.5 | 283 | 1.30 M NaCl, 0.1 M citric acid |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 3.27 | 62 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 126.469 | α = 90 |
| b = 126.469 | β = 90 |
| c = 126.469 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 41 3 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 | PIXEL | DECTRIS EIGER R 4M | | 2020-08-10 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 293 | AREA DETECTOR | ORNL ANGER CAMERA | | 2020-08-08 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54 | | |
| 2 | SPALLATION SOURCE | ORNL Spallation Neutron Source BEAMLINE MANDI | 3.0-5.0 | 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 | 30.67 | 99.87 | | | 0.1851 | 0.0571 | 0.988 | | 14.16 | 10.3 | | 20749 | | | |
| 1 | 2.8 | 14.8 | 99.3 | | | 0.275 | 0.081 | 0.92 | | 10.1 | 10.2 | | 8942 | | | |
| 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 | 2.8 | 2.9 | | | | | 0.4802 | 0.746 | | | | |
| 1 | 2.8 | 2.9 | | | | | 0.102 | 0.348 | | | | |
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 | 2.1 | 30.67 | | 1.35 | | 20738 | 1033 | 99.92 | | 0.1496 | 0.1484 | 0.15 | 0.1702 | 0.17 | | 33.56 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.8 | 14.8 | | | | 8942 | | 99.3 | | | 0.2251 | | 0.2598 | | | |
| 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 | 19.7214 |
| f_angle_d | 2.3566 |
| f_chiral_restr | 0.0728 |
| f_bond_d | 0.0301 |
| f_plane_restr | 0.0085 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1788 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 117 |
| Heterogen Atoms | 16 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| Mantid | data reduction |
| LAUENORM | data scaling |
| PHASER | phasing |
