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The structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum with molecular oxygen at 1.05 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OEX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 0.2 M sodium formate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.2 44.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.84 α = 90 b = 96.57 β = 90 c = 147.45 γ = 90
Symmetry Space Group P 21 21 21
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 2021-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.7 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 1.05 50 99.9 0.059000000000000004 0.064 0.9990000000000001 14.21 6.8 441007
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 1.05 1.1 0.8079999999999999 0.875 0.775
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 1.05 45.93 419044 21961 99.93 0.10933 0.10846 0.1105 0.12583 0.1277 RANDOM 14.395
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] 0.39 -0.27 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.788 r_dihedral_angle_4_deg 18.957 r_dihedral_angle_3_deg 10.903 r_rigid_bond_restr 8.277 r_dihedral_angle_1_deg 7.268 r_long_range_B_refined 3.019 r_long_range_B_other 2.799 r_scangle_other 2.762 r_scbond_it 2.261 r_scbond_other 2.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.788 r_dihedral_angle_4_deg 18.957 r_dihedral_angle_3_deg 10.903 r_rigid_bond_restr 8.277 r_dihedral_angle_1_deg 7.268 r_long_range_B_refined 3.019 r_long_range_B_other 2.799 r_scangle_other 2.762 r_scbond_it 2.261 r_scbond_other 2.258 r_mcangle_it 2.209 r_mcangle_other 2.209 r_mcbond_it 2.078 r_mcbond_other 2.078 r_angle_refined_deg 1.865 r_angle_other_deg 0.818 r_chiral_restr 0.129 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7278 Nucleic Acid Atoms Solvent Atoms 1319 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction MOLREP phasing