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The structure of non-activated thiocyanate dehydrogenase from Pelomicrobium methylotrophicum (pmTcDH)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8Q9X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 0.1 M HEPES, pH 7.5, 21% PEG 8000, 8% Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.25 45.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.99 α = 90 b = 101.95 β = 90 c = 276.17 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 X 16M 2023-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17UM 0.9792 SSRF BL17UM
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 1.45 50 99.5 0.068 0.071 0.9990000000000001 20.31 13.1 243938
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 1.45 1.5 1.014 1.055 0.828
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 8Q9X 1.45 49.04 229928 11984 99.52 0.16809 0.16663 0.1727 0.19625 0.2015 RANDOM 20.081
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] 0.6 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.508 r_dihedral_angle_4_deg 19.153 r_dihedral_angle_3_deg 13.272 r_dihedral_angle_1_deg 7.473 r_long_range_B_refined 4.128 r_scbond_it 2.724 r_mcangle_it 2.379 r_angle_refined_deg 2.259 r_mcbond_it 1.798 r_chiral_restr 0.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.508 r_dihedral_angle_4_deg 19.153 r_dihedral_angle_3_deg 13.272 r_dihedral_angle_1_deg 7.473 r_long_range_B_refined 4.128 r_scbond_it 2.724 r_mcangle_it 2.379 r_angle_refined_deg 2.259 r_mcbond_it 1.798 r_chiral_restr 0.148 r_gen_planes_refined 0.017 r_bond_refined_d 0.016 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 10800 Nucleic Acid Atoms Solvent Atoms 1325 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction MOLREP phasing