High-resolution neutron and X-ray joint refined structure of high-potential iron-sulfur protein in the oxidized state
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 5WQQ | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 293 | 1.8M ammonium sulfate, 0.1M Na citrate buffer |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 1.83 | 32.62 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 46.334 | α = 90 |
| b = 58.855 | β = 90 |
| c = 23.548 | 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 | 100 | CCD | ADSC QUANTUM 315r | | 2014-06-10 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 100 | DIFFRACTOMETER | iBIX | | 2014-05-13 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 0.7500 | Photon Factory | BL-5A |
| 2 | SPALLATION SOURCE | J-PARC MLF BEAMLINE BL-03 | 2.00-4.40 | 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 | 0.66 | 50 | 96.3 | 0.059 | | | | | | 45.4 | 7.4 | | 117107 | | | 3.81 |
| 2 | 1.2 | 20 | 94.9 | 0.21 | | | | | | 6 | 4.8 | | 19669 | | | 3.81 |
| 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 | 0.66 | 0.67 | | 0.272 | | | | | | 4.5 | 4.8 | |
| 2 | 1.2 | 1.24 | | 0.4 | | | | | | 2.1 | 2.5 | |
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 | 0.66 | 36.41 | | 1.51 | | 117020 | 5799 | 96.3 | | 0.074 | 0.074 | 0.07 | 0.082 | 0.08 | | |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.2 | 15.07 | | | | 19667 | | 94.6 | | 0.154 | 0.154 | | 0.168 | | | |
| 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 | 616 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 129 |
| Heterogen Atoms | 68 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| SCALA | data scaling |
| MOLREP | phasing |
| HKL-2000 | data collection |
