High-resolution neutron and X-ray joint refined structure of copper-containing nitrite reductase from Geobacillus thermodenitrificans
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Crystallization
Crystalization Experiments |
---|
ID | Method | pH | Temperature | Details |
---|
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 293 | 0.1 M acetate buffer pH 4.6, 5.5% (w/v) PEG 4000, and 50 mM CuSO4 |
Crystal Properties |
---|
Matthews coefficient | Solvent content |
---|
2.96 | 58.41 |
Crystal Data
Unit Cell |
---|
Length ( Å ) | Angle ( ˚ ) |
---|
a = 114.212 | α = 90 |
b = 114.212 | β = 90 |
c = 83.688 | γ = 120 |
Diffraction
Diffraction Experiment |
---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
---|
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 2M-F | | 2018-12-16 | M | SINGLE WAVELENGTH |
2 | 1 | neutron | 100 | DIFFRACTOMETER | iBIX | | 2018-11-26 | L | LAUE |
Radiation Source |
---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
---|
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NE3A | 1.0000 | Photon Factory | AR-NE3A |
2 | SPALLATION SOURCE | J-PARC MLF BEAMLINE BL-03 | 2.15-4.89 | 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 | 1.03 | 42.58 | 99.9 | 0.065 | | | 0.021 | | | 21.2 | 9.6 | | 201251 | | | |
2 | 1.5 | 17.38 | 99.7 | 0.23 | | | 0.097 | | | 9.5 | 6.6 | | 64997 | | | 6.1 |
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 | 1.03 | 1.05 | | 0.641 | | | 0.253 | 0.907 | | 3.5 | 7.1 | |
2 | 1.5 | 1.59 | | 0.608 | | | 0.285 | 0.782 | | 2.2 | 5.3 | |
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 | R-Free | R-Free Selection Details | Mean Isotropic B |
---|
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.3 | 34.13 | | 2 | | 100127 | 2516 | 100 | | 0.0978 | 0.0973 | 0.1117 | | 15.48 |
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.5 | 17.071 | | | | 64964 | 2006 | 99.69 | | 0.1421 | 0.1416 | 0.1586 | | |
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 | 21.0391 |
f_dihedral_angle_d | 21.0391 |
f_angle_d | 1.0535 |
f_angle_d | 1.0535 |
f_chiral_restr | 0.0904 |
f_chiral_restr | 0.0904 |
f_bond_d | 0.008 |
f_bond_d | 0.008 |
f_plane_restr | 0.0075 |
f_plane_restr | 0.0075 |
Non-Hydrogen Atoms Used in Refinement |
---|
Non-Hydrogen Atoms | Number |
---|
Protein Atoms | 2314 |
Nucleic Acid Atoms | |
Solvent Atoms | 458 |
Heterogen Atoms | 14 |
Software
Software |
---|
Software Name | Purpose |
---|
PHENIX | refinement |
SCALA | data scaling |
MOLREP | phasing |
PDB_EXTRACT | data extraction |
STARGazer | data reduction |