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Crystal structure of a Sulfite dehydrogenase from Thermus thermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y0K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 14% PEG 8000, 0.1 M sodium citrate tribasic dihydrate pH 5.5
Crystal Properties Matthews coefficient Solvent content 3.25 62.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.02 α = 90 b = 130.02 β = 90 c = 114.79 γ = 120
Symmetry Space Group P 61 2 2
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 2019-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96851 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.85 42.56 99.94 0.02516 0.999 16.83 12.2 49202 31.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.916 99.96 0.3857 0.733 2.46 12.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.85 42.559 49202 2000 99.961 0.166 0.1653 0.1765 0.192 0.1992 33.1
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] -0.295 -0.147 -0.295 0.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.567 r_dihedral_angle_3_deg 12.848 r_dihedral_angle_2_deg 9.001 r_lrange_it 8.608 r_lrange_other 8.592 r_scangle_it 7.346 r_scangle_other 7.345 r_dihedral_angle_1_deg 6.647 r_scbond_it 4.921 r_scbond_other 4.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.567 r_dihedral_angle_3_deg 12.848 r_dihedral_angle_2_deg 9.001 r_lrange_it 8.608 r_lrange_other 8.592 r_scangle_it 7.346 r_scangle_other 7.345 r_dihedral_angle_1_deg 6.647 r_scbond_it 4.921 r_scbond_other 4.919 r_mcangle_other 3.85 r_mcangle_it 3.84 r_mcbond_it 3.022 r_mcbond_other 3.021 r_angle_refined_deg 1.926 r_angle_other_deg 0.617 r_nbd_refined 0.215 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.162 r_nbd_other 0.136 r_symmetry_xyhbond_nbd_refined 0.098 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.087 r_symmetry_nbd_refined 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_dihedral_angle_other_3_deg 0.003 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2974 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing