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The structure of thiocyanate dehydrogenase mutant form with Thr 169 replaced by Ala from Thioalkalivibrio paradoxus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I3Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 0.2 M (NH4)2SO4, 0.1 M Bis-Tris, pH5.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.64 53.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.81 α = 90 b = 162.24 β = 119.74 c = 90.76 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm 2019-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 0.793120 KURCHATOV SNC K4.4
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 1.8 81.12 98.8 0.252 0.273 0.987 6.57 6.7 208077
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 1.8 1.85 1.187 1.29 0.72
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 81.12 197378 10643 98.86 0.18986 0.18641 0.1904 0.25409 0.2575 RANDOM 18.867
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] -6.24 -2.52 29.47 -23.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.222 r_dihedral_angle_4_deg 20.372 r_dihedral_angle_3_deg 20.006 r_dihedral_angle_1_deg 10.301 r_long_range_B_refined 5.395 r_mcangle_it 3.882 r_scbond_it 3.233 r_mcbond_it 3.024 r_angle_refined_deg 3.001 r_chiral_restr 0.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.222 r_dihedral_angle_4_deg 20.372 r_dihedral_angle_3_deg 20.006 r_dihedral_angle_1_deg 10.301 r_long_range_B_refined 5.395 r_mcangle_it 3.882 r_scbond_it 3.233 r_mcbond_it 3.024 r_angle_refined_deg 3.001 r_chiral_restr 0.219 r_gen_planes_refined 0.022 r_bond_refined_d 0.018 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 Atoms Number Protein Atoms 14527 Nucleic Acid Atoms Solvent Atoms 743 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction MOLREP phasing