8Q9Y
The structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum in complex with inhibitor thiourea at 1.10 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 288 | 0.2 M sodium formate, 20% PEG 3350 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.2 | 44.05 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 66.71 | α = 90 |
b = 96.67 | β = 90 |
c = 147.53 | 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 | PIXEL | DECTRIS EIGER X 16M | 2021-07-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 0.7 | SPring-8 | BL41XU |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | 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 | 1.1 | 50 | 93 | 0.025 | 0.03 | 1 | 17.52 | 2.8 | 357145 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.1 | 1.15 | 0.321 | 0.395 | 0.8540000000000001 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.1 | 39.17 | 341358 | 15786 | 92.98 | 0.10814 | 0.10729 | 0.1246 | RANDOM | 16.204 |
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] | |
-0.61 | 1.4 | -0.79 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.086 |
r_dihedral_angle_4_deg | 18.219 |
r_dihedral_angle_3_deg | 11.141 |
r_dihedral_angle_1_deg | 7.224 |
r_rigid_bond_restr | 6.589 |
r_long_range_B_refined | 3.5 |
r_long_range_B_other | 2.955 |
r_scangle_other | 2.657 |
r_scbond_it | 2.396 |
r_scbond_other | 2.395 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 7283 |
Nucleic Acid Atoms | |
Solvent Atoms | 1285 |
Heterogen Atoms | 25 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XSCALE | data scaling |
XDS | data reduction |
MOLREP | phasing |