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Crystal structure of mouse cytosolic sulfotransferase mSULT1D1 complex with PAP and alpha-naphthol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZPT PDB ENTRY 2ZPT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 16% PEG 10000, 10mM dithiothreitol, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.1 60.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.178 α = 90 b = 67.49 β = 105.47 c = 42.821 γ = 90
Symmetry Space Group C 1 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 CCD RIGAKU JUPITER 210 mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
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 1.23 50 77.6 0.061 0.061 13.4 3.2 96125 96125 13.5
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) 1 1.23 9 0.743 0.743 1.2
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 (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 PDB ENTRY 2ZPT 1.3 21.41 89190 4677 89.28 0.17221 0.17137 0.1698 0.18819 0.1862 RANDOM 13.524
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.299 r_dihedral_angle_4_deg 20.588 r_dihedral_angle_3_deg 12.674 r_dihedral_angle_1_deg 5.216 r_scangle_it 2.567 r_scbond_it 1.696 r_angle_refined_deg 1.279 r_mcangle_it 1.06 r_mcbond_it 0.665 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.299 r_dihedral_angle_4_deg 20.588 r_dihedral_angle_3_deg 12.674 r_dihedral_angle_1_deg 5.216 r_scangle_it 2.567 r_scbond_it 1.696 r_angle_refined_deg 1.279 r_mcangle_it 1.06 r_mcbond_it 0.665 r_nbtor_refined 0.318 r_symmetry_vdw_refined 0.259 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.12 r_xyhbond_nbd_refined 0.106 r_chiral_restr 0.086 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2414 Nucleic Acid Atoms Solvent Atoms 424 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement BBS data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing