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The structure of non-activated thiocyanate dehydrogenase mutant with the H447Q substitution from Pelomicrobium methylotrophicum (pmTcDH H447Q)
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 0.1M HEPES, pH 7.5, 20% PEG 8000, 8% Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.2 44.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.77 α = 90 b = 96.44 β = 90 c = 147.67 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 EIGER2 X 16M 2023-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17UM 0.979 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 97.6 0.061 0.066 0.9990000000000001 19.01 6.7 164827
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 0.56 0.609 0.865
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 1.45 45.88 156611 8215 97.55 0.15074 0.14958 0.1538 0.17314 0.1764 RANDOM 16.041
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] 0.33 -0.03 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.452 r_dihedral_angle_4_deg 19.033 r_dihedral_angle_3_deg 11.465 r_dihedral_angle_1_deg 7.251 r_long_range_B_refined 3.727 r_scbond_it 2.172 r_angle_refined_deg 2.018 r_mcangle_it 1.805 r_mcbond_it 1.301 r_chiral_restr 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.452 r_dihedral_angle_4_deg 19.033 r_dihedral_angle_3_deg 11.465 r_dihedral_angle_1_deg 7.251 r_long_range_B_refined 3.727 r_scbond_it 2.172 r_angle_refined_deg 2.018 r_mcangle_it 1.805 r_mcbond_it 1.301 r_chiral_restr 0.134 r_bond_refined_d 0.014 r_gen_planes_refined 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 7236 Nucleic Acid Atoms Solvent Atoms 1044 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction MOLREP phasing