6SJI

The structure of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus mutant with His 482 replaced by Gln


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OEX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52940.17M Ammonium acetate, 0.085 M Sodium cacjdilate pH 6.5, 25.5 % v/v Polyatilen glycol 8000, 15% v/v glycerol
Crystal Properties
Matthews coefficientSolvent content
2.4349.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.08α = 90
b = 160.41β = 98.114
c = 90.88γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.968623ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.89096.20.1220.9876.632.7176251
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.85980.4560.8242.22.57

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5OEX1.889.97176251876196.2530.1610.15910.198423.99
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]
0.112-1.1280.1760.032
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.672
r_dihedral_angle_4_deg20.739
r_sphericity_bonded16.629
r_dihedral_angle_3_deg13.884
r_dihedral_angle_1_deg7.447
r_lrange_it5.394
r_scangle_it4.336
r_scbond_it3.011
r_mcangle_it2.538
r_angle_refined_deg1.937
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.672
r_dihedral_angle_4_deg20.739
r_sphericity_bonded16.629
r_dihedral_angle_3_deg13.884
r_dihedral_angle_1_deg7.447
r_lrange_it5.394
r_scangle_it4.336
r_scbond_it3.011
r_mcangle_it2.538
r_angle_refined_deg1.937
r_mcbond_it1.897
r_nbtor_refined0.306
r_symmetry_nbd_refined0.253
r_nbd_refined0.197
r_chiral_restr0.145
r_symmetry_xyhbond_nbd_refined0.139
r_xyhbond_nbd_refined0.119
r_bond_refined_d0.02
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14585
Nucleic Acid Atoms
Solvent Atoms1183
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing