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The structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum in complex with inhibitor thiourea at 1.10 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 44.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.71 α = 90 b = 96.67 β = 90 c = 147.53 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 1.1 50 93 0.025 0.03 1 17.52 2.8 357145
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 1.1 1.15 0.321 0.395 0.8540000000000001
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 1.1 39.17 341358 15786 92.98 0.10814 0.10729 0.106 0.1246 0.1499 RANDOM 16.204
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] -0.61 1.4 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.086 r_dihedral_angle_4_deg 18.219 r_dihedral_angle_3_deg 11.141 r_dihedral_angle_1_deg 7.224 r_rigid_bond_restr 6.589 r_long_range_B_refined 3.5 r_long_range_B_other 2.955 r_scangle_other 2.657 r_scbond_it 2.396 r_scbond_other 2.395
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.086 r_dihedral_angle_4_deg 18.219 r_dihedral_angle_3_deg 11.141 r_dihedral_angle_1_deg 7.224 r_rigid_bond_restr 6.589 r_long_range_B_refined 3.5 r_long_range_B_other 2.955 r_scangle_other 2.657 r_scbond_it 2.396 r_scbond_other 2.395 r_angle_refined_deg 1.969 r_mcangle_it 1.836 r_mcangle_other 1.836 r_mcbond_it 1.427 r_mcbond_other 1.427 r_angle_other_deg 0.726 r_chiral_restr 0.137 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 7283 Nucleic Acid Atoms Solvent Atoms 1285 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction MOLREP phasing