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The structure of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus complex with CU(I) ions.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F30
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 PROTEIN SOLUTION: 10 MG/ML PROTEIN, 25
MM BORATE BUFFER (PH 9.5)
Reservoir solution: 0.2 sodium malonate pH 6.0,
20% w/v PEG 3350.
Prior to data collection crystal additionally treated by a mixture of 0.2 mM Cu(2+) and 5 mM ascorbate to increase copper incorporation.
Crystal Properties Matthews coefficient Solvent content 2.8 56.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.64 α = 90 b = 162.37 β = 119.64 c = 90.71 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 PILATUS3 6M 2015-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.31 45.58 95.7 0.101 0.993 9.34 2.53 95620
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.31 2.45 91 0.548 0.741 2.36 2.32
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 5f30 2.31 45.58 91028 4591 95.85 0.13591 0.1323 0.1369 0.20622 0.2095 RANDOM 37.564
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] -9.73 -0.71 18.54 -8.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.955 r_dihedral_angle_4_deg 20.138 r_sphericity_bonded 19.812 r_dihedral_angle_3_deg 18.016 r_dihedral_angle_1_deg 8.805 r_mcangle_it 4.727 r_scbond_it 3.832 r_mcbond_it 3.399 r_angle_refined_deg 2.145 r_chiral_restr 0.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.955 r_dihedral_angle_4_deg 20.138 r_sphericity_bonded 19.812 r_dihedral_angle_3_deg 18.016 r_dihedral_angle_1_deg 8.805 r_mcangle_it 4.727 r_scbond_it 3.832 r_mcbond_it 3.399 r_angle_refined_deg 2.145 r_chiral_restr 0.144 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 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_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14516 Nucleic Acid Atoms Solvent Atoms 912 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing