Neutron structure of [NiFe]-hydrogenase from D. vulgaris Miyazaki F in its oxidized state
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 4U9H | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 7 | 283 | 30%(v/v) 2-methyl-2,4-pentane-d12-diol, 10 mM glucose-d12, 25 mM Tris-d11-DCl in D2O |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.34 | 47.5 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 66.705 | α = 90 |
| b = 98.485 | β = 90 |
| c = 126.86 | 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 | RAYONIX MX225HE | | 2015-04-10 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 100 | DIFFRACTOMETER | iBIX | | 2015-03-21 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B1 | 0.8000 | SPring-8 | BL26B1 |
| 2 | SPALLATION SOURCE | J-PARC MLF BEAMLINE BL-03 | 1.8-5.8 | 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 | 1.04 | 50 | 99.9 | 0.059 | | 0.062 | | 1 | | 19.7 | 8.5 | | 397623 | | | |
| 2 | 2.2 | 20 | 90.1 | 0.22 | | 0.266 | | 0.92 | | 4.9 | 2.6 | | 38335 | | | |
| 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 | 1.04 | 1.07 | | 0.461 | | 0.496 | | 0.924 | | 4.1 | 7.2 | |
| 2 | 2.2 | 2.32 | | 0.394 | | 0.473 | | 0.57 | | 2.3 | 2.8 | |
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 | 1.04 | 41.69 | | 1.34 | | 397425 | 19868 | 99.78 | | 0.143 | 0.1428 | 0.1426 | 0.1474 | 0.1472 | | |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.2 | 17.94 | | | | 38312 | 1893 | 88.91 | | 0.1909 | 0.1893 | | 0.2202 | | | |
| 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 | 18.819 |
| f_dihedral_angle_d | 18.819 |
| f_angle_d | 1.213 |
| f_angle_d | 1.213 |
| f_chiral_restr | 0.095 |
| f_chiral_restr | 0.095 |
| f_bond_d | 0.014 |
| f_bond_d | 0.014 |
| f_plane_restr | 0.008 |
| f_plane_restr | 0.008 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 6188 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 842 |
| Heterogen Atoms | 106 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| STARGazer | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
