Neutron structure of Bacillus thermoproteolyticus Ferredoxin at room temperature
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1IQZ | 1IQZ 1IQZ |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | MICRODIALYSIS | | 277 | MES, ammonium sulfate |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.41 | 49.06 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 70.43 | α = 90 |
| b = 37.91 | β = 105.96 |
| c = 33.01 | γ = 90 |
| Symmetry |
|---|
| Space Group | C 1 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 | 297 | CCD | ADSC QUANTUM 270 | | 2018-12-10 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 297 | DIFFRACTOMETER | iBIX | | 2018-11-02 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NW12A | 1.0 | Photon Factory | AR-NW12A |
| 2 | SPALLATION SOURCE | J-PARC MLF BEAMLINE BL-03 | 1.5-4.5 | JPARC MLF | BL-03 |
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 | 1.45 | 50 | 100 | | | | | 0.999 | | 25.2 | 6.7 | | 15007 | | | 16.15 |
| 2 | 1.6 | 15.87 | 99.6 | 0.1976 | 0.0685 | | | | | 5.15 | 7.5617 | | 84041 | | | 16.15 |
| 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 | 1.45 | 1.48 | | | | | | 0.894 | | | | |
| 2 | 1.6 | 1.66 | | 0.4602 | | | 0.1926 | | | | | |
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 | 1.45 | 33.08 | | 1.38 | | 14861 | 771 | 98.87 | | 0.1399 | 0.139 | 0.14 | 0.1572 | 0.16 | | 25.52 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.6 | 15.12 | | | | 10500 | | 94.13 | | | 0.1624 | | 0.1842 | | | |
| 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 | 17.2996 |
| f_angle_d | 1.0652 |
| f_chiral_restr | 0.1093 |
| f_bond_d | 0.0107 |
| f_plane_restr | 0.0081 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 608 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 66 |
| Heterogen Atoms | 8 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| REFMAC | phasing |
