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Crystal structure of human tyrosylprotein sulfotransferase-1 complexed with PAP and gastrin peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WRI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M potassium sodium tartrate trihydrate, 19.5% w/v polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.99 58.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.668 α = 90.6 b = 93.263 β = 93.39 c = 93.012 γ = 103.39
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-225 2015-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.000 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.33 50 97.5 0.155 8.33 1.9 71093
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 (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 5WRI 2.31 48.99 67464 3560 95.92 0.2424 0.24096 0.2392 0.26943 0.2667 RANDOM 46.267
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.406 r_dihedral_angle_3_deg 13.746 r_dihedral_angle_4_deg 11.896 r_dihedral_angle_1_deg 5.055 r_long_range_B_refined 3.612 r_long_range_B_other 3.594 r_angle_other_deg 3.563 r_scangle_other 2.05 r_mcangle_it 1.955 r_mcangle_other 1.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.406 r_dihedral_angle_3_deg 13.746 r_dihedral_angle_4_deg 11.896 r_dihedral_angle_1_deg 5.055 r_long_range_B_refined 3.612 r_long_range_B_other 3.594 r_angle_other_deg 3.563 r_scangle_other 2.05 r_mcangle_it 1.955 r_mcangle_other 1.955 r_scbond_it 1.194 r_scbond_other 1.194 r_angle_refined_deg 1.175 r_mcbond_it 1.162 r_mcbond_other 1.162 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8872 Nucleic Acid Atoms 108 Solvent Atoms 144 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing