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The structure of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus as isolated.
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 5.5 290 PRECIPITANT SOLUTION: 0.2 M lithium
sulfate, 0.1 M BIS-TRIS, pH 5.5, 25% w/v PEG 3350.
Protein solution: TcDH 10 mg/ml 25 mM borate, pH 9.5
Crystal Properties Matthews coefficient Solvent content 2.8 56.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.63 α = 90 b = 162.28 β = 119.51 c = 90.57 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 2016-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.98400 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 1.65 45.4 97.3 0.098 0.996 9.2 2.6 691361
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 1.65 1.7 96.8 0.79 0.51 1.65
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 FOURIER SYNTHESIS THROUGHOUT 5F30 1.65 45.31 238854 26618 97.3 0.14699 0.14261 0.1517 0.20716 0.1436 RANDOM 19.444
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] -4.43 -0.36 8.37 -3.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.268 r_dihedral_angle_4_deg 20.494 r_dihedral_angle_3_deg 14.413 r_sphericity_free 12.756 r_sphericity_bonded 10.831 r_dihedral_angle_1_deg 7.862 r_long_range_B_refined 4.121 r_scbond_it 1.982 r_mcangle_it 1.939 r_angle_refined_deg 1.901
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.268 r_dihedral_angle_4_deg 20.494 r_dihedral_angle_3_deg 14.413 r_sphericity_free 12.756 r_sphericity_bonded 10.831 r_dihedral_angle_1_deg 7.862 r_long_range_B_refined 4.121 r_scbond_it 1.982 r_mcangle_it 1.939 r_angle_refined_deg 1.901 r_mcbond_it 1.407 r_chiral_restr 0.133 r_bond_refined_d 0.016 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_other r_rigid_bond_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14572 Nucleic Acid Atoms Solvent Atoms 1531 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling Coot model building MOLREP phasing