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Crystal structure of mouse cytosolic sulfotransferase mSULT1D1 complex with PAPS
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 3.37 63.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.156 α = 90 b = 65.154 β = 104.2 c = 46.824 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 1.55 50 81.4 0.093 0.093 14.2 3.2 55335 55335
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 1.55 1.61 42.8 0.527 0.527 1.2 2.5 2890
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 1.55 34.67 52526 2782 81.29 0.19193 0.19097 0.1891 0.21 0.209 RANDOM 22.943
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 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.094 r_dihedral_angle_4_deg 19.716 r_dihedral_angle_3_deg 12.737 r_dihedral_angle_1_deg 5.117 r_scangle_it 2.275 r_scbond_it 1.463 r_angle_refined_deg 1.2 r_mcangle_it 0.946 r_mcbond_it 0.593 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.094 r_dihedral_angle_4_deg 19.716 r_dihedral_angle_3_deg 12.737 r_dihedral_angle_1_deg 5.117 r_scangle_it 2.275 r_scbond_it 1.463 r_angle_refined_deg 1.2 r_mcangle_it 0.946 r_mcbond_it 0.593 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.204 r_nbd_refined 0.192 r_symmetry_hbond_refined 0.115 r_xyhbond_nbd_refined 0.104 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2440 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement BBS data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing