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Crystal structure of recombinant thiocyanate dehydrogenase from Thioalkalivibrio paradoxus saturated with copper
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I3Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 10 mg/mL TcDH in 25 mM borate buffer, pH 9.5 was mixed with 0.17 M ammonium acetate, 0.085 M sodium citrate, pH 5.6, 25.5% w/v PEG 4000, 15% glycerol. To increase copper incorporation, powder of CuCl was added to drops with crystals 30-40 min prior to harvesting. Sodium cyanate solution was added to the drop with crystals to the final concertation of ~100 mM at the same time as CuCl was added.
Crystal Properties Matthews coefficient Solvent content 2.8 56.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.422 α = 90 b = 163.149 β = 119.29 c = 90.631 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS 6M 2017-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.96900 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim 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 1.6 50 94.4 0.074 0.074 0.092 0.053 0.993 9.3 2.6 285581 -3 15.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 92.6 0.461 0.461 0.575 0.341 0.692 2.1 2.6
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 6I3Q 1.6 44.8 261930 13391 90.98 0.1424 0.1415 0.1504 0.1602 0.168 RANDOM 15.065
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] -0.32 0.38 1.41 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.656 r_dihedral_angle_1_deg 20.132 r_dihedral_angle_4_deg 20.011 r_dihedral_angle_3_deg 12.342 r_angle_refined_deg 1.511 r_angle_other_deg 1.38 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.656 r_dihedral_angle_1_deg 20.132 r_dihedral_angle_4_deg 20.011 r_dihedral_angle_3_deg 12.342 r_angle_refined_deg 1.511 r_angle_other_deg 1.38 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14560 Nucleic Acid Atoms Solvent Atoms 2369 Heterogen Atoms 30
Software Software Software Name Purpose SCALEPACK data scaling HKL-3000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction MOLREP phasing Coot refinement