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Sulfite oxidase from Thermus thermophilus with coordinated phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BLF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 1.8 Na/K phosphate
Crystal Properties Matthews coefficient Solvent content 3.27 62.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.6 α = 90 b = 130.6 β = 90 c = 114.59 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 2018-10-21 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) 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 1.7 42.75 99.94 0.08164 0.02249 0.999 18.68 13.6 63544 25.29
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 1.7 1.76 100 1.063 0.2857 0.826 2.67 14
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2BLF 1.7 42.749 63543 2000 99.967 0.167 0.1658 0.1775 0.1909 0.1961 26.697
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] 0.345 0.172 0.345 -1.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.484 r_dihedral_angle_4_deg 16.353 r_dihedral_angle_3_deg 12.414 r_dihedral_angle_1_deg 6.655 r_lrange_it 6.216 r_lrange_other 6.216 r_scangle_it 4.145 r_scangle_other 4.144 r_scbond_it 2.742 r_scbond_other 2.741
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.484 r_dihedral_angle_4_deg 16.353 r_dihedral_angle_3_deg 12.414 r_dihedral_angle_1_deg 6.655 r_lrange_it 6.216 r_lrange_other 6.216 r_scangle_it 4.145 r_scangle_other 4.144 r_scbond_it 2.742 r_scbond_other 2.741 r_mcangle_other 2.205 r_mcangle_it 2.204 r_mcbond_it 1.571 r_mcbond_other 1.568 r_angle_refined_deg 1.498 r_angle_other_deg 1.333 r_nbd_other 0.31 r_symmetry_nbd_refined 0.291 r_nbd_refined 0.271 r_symmetry_nbd_other 0.185 r_symmetry_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.122 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2964 Nucleic Acid Atoms Solvent Atoms 418 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing