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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 295 0.15 M potassium bromide, 30% w/v polyethylene glycol monomethyl ether 2000
Crystal Properties Matthews coefficient Solvent content 2.26 45.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.286 α = 90 b = 83.286 β = 90 c = 115.793 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 2.23 40 99.2 0.128 0.128 0.172 0.057 0.997 15.14 9.1 23149
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 2.23 2.27 99.6 0.907 0.907 0.858 0.339 0.738 2 6.2
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 2.23 39.217 23020 1205 99.19 0.176 0.1738 0.1784 0.2252 0.2243 33.47
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] 1.13 0.565 1.13 -3.664
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.014 r_dihedral_angle_3_deg 12.44 r_dihedral_angle_4_deg 11.544 r_dihedral_angle_1_deg 6.433 r_lrange_it 6.29 r_lrange_other 6.134 r_scangle_it 1.901 r_scangle_other 1.901 r_mcangle_it 1.831 r_mcangle_other 1.831
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.014 r_dihedral_angle_3_deg 12.44 r_dihedral_angle_4_deg 11.544 r_dihedral_angle_1_deg 6.433 r_lrange_it 6.29 r_lrange_other 6.134 r_scangle_it 1.901 r_scangle_other 1.901 r_mcangle_it 1.831 r_mcangle_other 1.831 r_angle_refined_deg 1.382 r_angle_other_deg 1.331 r_scbond_it 1.105 r_scbond_other 1.105 r_mcbond_it 1.042 r_mcbond_other 1.039 r_symmetry_nbd_refined 0.248 r_symmetry_metal_ion_refined 0.236 r_nbd_refined 0.209 r_nbd_other 0.196 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.164 r_metal_ion_refined 0.139 r_xyhbond_nbd_refined 0.135 r_symmetry_xyhbond_nbd_refined 0.1 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.067 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3495 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-3000 data scaling MOLREP phasing