6UWE

Crystal structure of recombinant thiocyanate dehydrogenase from Thioalkalivibrio paradoxus saturated with copper


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6I3Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29310 mg/mL TcDH in 25 mM borate buffer, pH 9.5 was mixed with 0.17 M ammonium acetate, 0.085 M sodium citrate, pH 5.6, 25.5% w/v PEG 4000, 15% glycerol. To increase copper incorporation, powder of CuCl was added to drops with crystals 30-40 min prior to harvesting. Sodium cyanate solution was added to the drop with crystals to the final concertation of ~100 mM at the same time as CuCl was added.
Crystal Properties
Matthews coefficientSolvent content
2.856.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.422α = 90
b = 163.149β = 119.29
c = 90.631γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.96900ESRFID29

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)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
11.65094.40.0740.0740.0920.0530.9939.32.6285581-315.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6392.60.4610.4610.5750.3410.6922.12.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT6I3Q1.644.82619301339190.980.14240.14150.1602RANDOM15.065
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]
-0.320.381.41-1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.656
r_dihedral_angle_1_deg20.132
r_dihedral_angle_4_deg20.011
r_dihedral_angle_3_deg12.342
r_angle_refined_deg1.511
r_angle_other_deg1.38
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.656
r_dihedral_angle_1_deg20.132
r_dihedral_angle_4_deg20.011
r_dihedral_angle_3_deg12.342
r_angle_refined_deg1.511
r_angle_other_deg1.38
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14560
Nucleic Acid Atoms
Solvent Atoms2369
Heterogen Atoms30

Software

Software
Software NamePurpose
SCALEPACKdata scaling
HKL-3000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
MOLREPphasing
Cootrefinement