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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 6UST
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 2.4 M sodium malonate pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.28 46.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.62 α = 90 b = 83.62 β = 90 c = 116.052 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 100 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 1.6 40 95.7 0.068 0.068 0.079 0.024 0.996 35.25 10.6 59449 -3
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 1.6 1.63 67.5 0.449 0.449 0.487 0.186 0.859 2 5.8
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 6UST 1.603 39.366 59345 3033 95.528 0.149 0.1476 0.1618 0.1779 0.1915 22.307
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] 0.348 0.174 0.348 -1.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.706 r_dihedral_angle_4_deg 16.984 r_dihedral_angle_3_deg 12.265 r_dihedral_angle_1_deg 5.968 r_lrange_it 5.55 r_lrange_other 5.387 r_scangle_it 3.548 r_scangle_other 3.547 r_angle_other_deg 2.361 r_scbond_it 2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.706 r_dihedral_angle_4_deg 16.984 r_dihedral_angle_3_deg 12.265 r_dihedral_angle_1_deg 5.968 r_lrange_it 5.55 r_lrange_other 5.387 r_scangle_it 3.548 r_scangle_other 3.547 r_angle_other_deg 2.361 r_scbond_it 2.29 r_scbond_other 2.289 r_mcangle_it 2.156 r_mcangle_other 2.156 r_angle_refined_deg 1.842 r_mcbond_it 1.445 r_mcbond_other 1.443 r_symmetry_nbd_refined 0.253 r_symmetry_xyhbond_nbd_refined 0.237 r_nbd_refined 0.223 r_symmetry_nbd_other 0.213 r_nbd_other 0.213 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.147 r_symmetry_metal_ion_refined 0.127 r_metal_ion_refined 0.119 r_chiral_restr 0.105 r_xyhbond_nbd_other 0.104 r_symmetry_nbtor_other 0.076 r_bond_other_d 0.035 r_gen_planes_other 0.02 r_bond_refined_d 0.014 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3501 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-3000 data scaling MOLREP phasing