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Crystal structure of sulfur oxygenase reductase from Sulfurisphaera tokodaii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CB2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.1 293 1.2 M ammonium sulfate, 100 mM MES-NaOH (pH 6.1), 4% dioxane
Crystal Properties Matthews coefficient Solvent content 3.92 68.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 299.806 α = 90 b = 299.806 β = 90 c = 299.806 γ = 90
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 S 6M 2019-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.73 48.7 100 0.126 0.028 0.999 17.4 20.7 460150 21.484
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.76 100 2.112 0.491 0.626 1.8 19.5
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 2CB2 1.73 48.68 437088 23051 99.99 0.1629 0.162 0.1734 0.1792 0.19 RANDOM 27.21
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.494 r_dihedral_angle_4_deg 20.863 r_dihedral_angle_3_deg 12.993 r_dihedral_angle_1_deg 7.122 r_angle_other_deg 2.288 r_angle_refined_deg 1.688 r_chiral_restr 0.098 r_bond_other_d 0.035 r_gen_planes_other 0.017 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.494 r_dihedral_angle_4_deg 20.863 r_dihedral_angle_3_deg 12.993 r_dihedral_angle_1_deg 7.122 r_angle_other_deg 2.288 r_angle_refined_deg 1.688 r_chiral_restr 0.098 r_bond_other_d 0.035 r_gen_planes_other 0.017 r_bond_refined_d 0.012 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20040 Nucleic Acid Atoms Solvent Atoms 1257 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing