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The structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum (pmTcDH), activated by crystals soaking with 1 mM CuCl2 during 6 months
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, 20% PEG 8000, 8% Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.12 41.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.8 α = 90 b = 101.75 β = 90 c = 276.35 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 1.8 50 98.8 0.10099999999999999 0.11 0.998 12.69 6.7 125833
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 1.126 1.217 0.679
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 1.8 47.79 119555 6278 98.78 0.16994 0.1675 0.1717 0.21728 0.2211 RANDOM 29.113
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] -1.56 2.11 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.365 r_dihedral_angle_4_deg 22.891 r_dihedral_angle_3_deg 14.338 r_dihedral_angle_1_deg 7.783 r_long_range_B_refined 6.016 r_scbond_it 4.248 r_mcangle_it 4.015 r_mcbond_it 3.406 r_angle_refined_deg 2.261 r_chiral_restr 0.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.365 r_dihedral_angle_4_deg 22.891 r_dihedral_angle_3_deg 14.338 r_dihedral_angle_1_deg 7.783 r_long_range_B_refined 6.016 r_scbond_it 4.248 r_mcangle_it 4.015 r_mcbond_it 3.406 r_angle_refined_deg 2.261 r_chiral_restr 0.169 r_gen_planes_refined 0.015 r_bond_refined_d 0.014 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 801 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction MOLREP phasing