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
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2880.2 M sodium formate, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.244.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.71α = 90
b = 96.67β = 90
c = 147.53γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.7SPring-8BL41XU

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.150930.0250.03117.522.8357145
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)RedundancyNumber Unique Reflections (All)
11.11.150.3210.3950.8540000000000001

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.139.173413581578692.980.108140.107290.1246RANDOM16.204
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]
-0.611.4-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.086
r_dihedral_angle_4_deg18.219
r_dihedral_angle_3_deg11.141
r_dihedral_angle_1_deg7.224
r_rigid_bond_restr6.589
r_long_range_B_refined3.5
r_long_range_B_other2.955
r_scangle_other2.657
r_scbond_it2.396
r_scbond_other2.395
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.086
r_dihedral_angle_4_deg18.219
r_dihedral_angle_3_deg11.141
r_dihedral_angle_1_deg7.224
r_rigid_bond_restr6.589
r_long_range_B_refined3.5
r_long_range_B_other2.955
r_scangle_other2.657
r_scbond_it2.396
r_scbond_other2.395
r_angle_refined_deg1.969
r_mcangle_it1.836
r_mcangle_other1.836
r_mcbond_it1.427
r_mcbond_other1.427
r_angle_other_deg0.726
r_chiral_restr0.137
r_bond_refined_d0.018
r_gen_planes_refined0.013
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7283
Nucleic Acid Atoms
Solvent Atoms1285
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing