8P3M

The structure of thiocyanate dehydrogenase mutant form with Lys 281 replaced by Ala from Thioalkalivibrio paradoxus


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2880.5 M (NH4)2SO4, 0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 0.7 M Li2SO4
Crystal Properties
Matthews coefficientSolvent content
2.3447.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.15α = 90
b = 142.42β = 90.07
c = 294.4γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.000000SPring-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
12.0749.1298.80.1250.1530.9916.912.92485243
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)
12.072.10.8130.9930.408

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 REPLACEMENTTHROUGHOUT2.0749.124607792446398.790.18160.178840.23365RANDOM30.317
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]
-0.73-0.26-0.090.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.8
r_dihedral_angle_4_deg19.914
r_dihedral_angle_3_deg17.296
r_dihedral_angle_1_deg8.725
r_long_range_B_refined8.106
r_scbond_it6.021
r_mcangle_it5.388
r_mcbond_it4.531
r_angle_refined_deg2.816
r_chiral_restr0.184
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.8
r_dihedral_angle_4_deg19.914
r_dihedral_angle_3_deg17.296
r_dihedral_angle_1_deg8.725
r_long_range_B_refined8.106
r_scbond_it6.021
r_mcangle_it5.388
r_mcbond_it4.531
r_angle_refined_deg2.816
r_chiral_restr0.184
r_bond_refined_d0.018
r_gen_planes_refined0.018
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms57885
Nucleic Acid Atoms
Solvent Atoms2420
Heterogen Atoms127

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing