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Crystal structure of sulfatase from Pedobacter yulinensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7STT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 0.1 M sodium citrate pH 5.5, 20% w/v polyethylene glycol 3000
Crystal Properties Matthews coefficient Solvent content 2.22 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.728 α = 90 b = 82.728 β = 90 c = 115.292 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 PIXEL DECTRIS EIGER X 16M 2021-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 2.34 40 98.8 0.101 0.101 0.148 0.048 0.998 18.5 9.2 19275
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.34 2.38 98.7 0.489 0.489 0.525 0.175 0.948 2 6.7
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 7STT 2.35 34.232 19228 943 98.353 0.174 0.1717 0.1773 0.2295 0.2244 56.402
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] 2.062 1.031 2.062 -6.691
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.863 r_dihedral_angle_4_deg 17.733 r_dihedral_angle_3_deg 13.266 r_dihedral_angle_1_deg 6.423 r_lrange_other 5.183 r_lrange_it 5.182 r_scangle_it 3.163 r_scangle_other 3.162 r_mcangle_it 2.86 r_mcangle_other 2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.863 r_dihedral_angle_4_deg 17.733 r_dihedral_angle_3_deg 13.266 r_dihedral_angle_1_deg 6.423 r_lrange_other 5.183 r_lrange_it 5.182 r_scangle_it 3.163 r_scangle_other 3.162 r_mcangle_it 2.86 r_mcangle_other 2.86 r_scbond_it 1.864 r_scbond_other 1.853 r_mcbond_it 1.719 r_mcbond_other 1.719 r_angle_refined_deg 1.313 r_angle_other_deg 1.271 r_nbd_other 0.28 r_symmetry_nbd_refined 0.242 r_symmetry_xyhbond_nbd_refined 0.224 r_nbd_refined 0.208 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.151 r_metal_ion_refined 0.141 r_symmetry_xyhbond_nbd_other 0.113 r_symmetry_nbtor_other 0.079 r_symmetry_metal_ion_refined 0.067 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3448 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-3000 data scaling MOLREP phasing