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Crystal structure of human tyrosylprotein sulfotransferase-1 complexed with PAP and C4 peptide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2 M trimethylamine N-oxide dihydrate, 0.1 M Tris-HCl, pH 8.5, 20% w/v polyethylene glycol monomethyl ether 2000
Crystal Properties Matthews coefficient Solvent content 2.01 38.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.576 α = 90 b = 155.972 β = 90 c = 48.892 γ = 90
Symmetry Space Group P 21 21 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 CCD RAYONIX MX225HE 2015-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.3 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 1.6 50 98 0.084 20.1 5.8 78540
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.6 31.34 74483 3941 97.68 0.13548 0.13327 0.1327 0.17807 0.1774 RANDOM 19.394
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 0.03 -0.04
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.734 r_dihedral_angle_2_deg 33.81 r_dihedral_angle_4_deg 15.105 r_dihedral_angle_3_deg 13.362 r_sphericity_bonded 7.76 r_dihedral_angle_1_deg 6.668 r_rigid_bond_restr 4.015 r_long_range_B_refined 3.244 r_long_range_B_other 2.928 r_mcangle_it 2.101
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.734 r_dihedral_angle_2_deg 33.81 r_dihedral_angle_4_deg 15.105 r_dihedral_angle_3_deg 13.362 r_sphericity_bonded 7.76 r_dihedral_angle_1_deg 6.668 r_rigid_bond_restr 4.015 r_long_range_B_refined 3.244 r_long_range_B_other 2.928 r_mcangle_it 2.101 r_mcangle_other 2.101 r_scangle_other 2.084 r_scbond_it 1.79 r_scbond_other 1.79 r_mcbond_it 1.645 r_mcbond_other 1.645 r_angle_refined_deg 1.516 r_angle_other_deg 1.028 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4499 Nucleic Acid Atoms Solvent Atoms 571 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing