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Crystal structure of a bacterial arylsulfate sulfotransferase catalytic intermediate with 4-methylumbelliferone bound in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ELQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 1.8M lithium sulfate, 0.1M sodium cacodylate, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.75 67.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.83 α = 90 b = 181.83 β = 90 c = 100.66 γ = 120
Symmetry Space Group P 32 1 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 PSI PILATUS 6M 2008-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.4 48 99.7 0.143 0.134 8.8 7.6 102818 102818 1 2.994 51.21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.53 100 0.55 0.51 3.7 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 3ELQ 2.4 38.43 2 72370 72370 1197 99.7 0.175 0.175 0.1804 0.216 0.221 RANDOM 41.17
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] -1.58 -0.79 -1.58 2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.151 r_dihedral_angle_3_deg 13.964 r_dihedral_angle_4_deg 13.816 r_scangle_it 7.078 r_dihedral_angle_1_deg 6.583 r_scbond_it 5.516 r_mcangle_it 3.508 r_mcbond_it 3.314 r_mcbond_other 1.769 r_angle_refined_deg 1.376
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.151 r_dihedral_angle_3_deg 13.964 r_dihedral_angle_4_deg 13.816 r_scangle_it 7.078 r_dihedral_angle_1_deg 6.583 r_scbond_it 5.516 r_mcangle_it 3.508 r_mcbond_it 3.314 r_mcbond_other 1.769 r_angle_refined_deg 1.376 r_angle_other_deg 0.982 r_symmetry_vdw_other 0.239 r_nbd_refined 0.235 r_nbd_other 0.232 r_symmetry_vdw_refined 0.229 r_nbtor_refined 0.189 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.12 r_chiral_restr 0.088 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8915 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 56
Software Software Software Name Purpose RemDAq data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling