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The structure of thiocyanate dehydrogenase mutant form with Lys 281 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 0.5 M (NH4)2SO4, 0.1 M Sodium citrate tribasic dihydrate, pH 5.6, 0.7 M Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.34 47.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.15 α = 90 b = 142.42 β = 90.07 c = 294.4 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 PIXEL DECTRIS EIGER X 16M 2019-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000000 SPring-8 BL41XU
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 2.07 49.12 98.8 0.125 0.153 0.991 6.91 2.92 485243
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 2.07 2.1 0.813 0.993 0.408
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.07 49.12 460779 24463 98.79 0.1816 0.17884 0.23365 0.2188 RANDOM 30.317
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 -0.09 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.8 r_dihedral_angle_4_deg 19.914 r_dihedral_angle_3_deg 17.296 r_dihedral_angle_1_deg 8.725 r_long_range_B_refined 8.106 r_scbond_it 6.021 r_mcangle_it 5.388 r_mcbond_it 4.531 r_angle_refined_deg 2.816 r_chiral_restr 0.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.8 r_dihedral_angle_4_deg 19.914 r_dihedral_angle_3_deg 17.296 r_dihedral_angle_1_deg 8.725 r_long_range_B_refined 8.106 r_scbond_it 6.021 r_mcangle_it 5.388 r_mcbond_it 4.531 r_angle_refined_deg 2.816 r_chiral_restr 0.184 r_bond_refined_d 0.018 r_gen_planes_refined 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 57885 Nucleic Acid Atoms Solvent Atoms 2420 Heterogen Atoms 127
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction MOLREP phasing