☰ Navigation Tabs
Crystal structure of mouse cytosolic sulfotransferase mSULT1D1 complex with PAPS and p-nitrophenyl sulfate
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 DTT, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.96 58.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.867 α = 90 b = 66.573 β = 106.1 c = 42.557 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 1.7 50 95.7 0.043 0.043 27.5 2.9 44210 44210
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 1.7 1.76 93.7 0.817 0.817 1.1 2.5 4301
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 1.8 24.66 34757 1865 96.15 0.19495 0.19338 0.1932 0.22359 0.2226 RANDOM 27.366
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 37.832 r_dihedral_angle_4_deg 19.647 r_dihedral_angle_3_deg 13.676 r_dihedral_angle_1_deg 5.599 r_scangle_it 2.984 r_scbond_it 1.896 r_angle_refined_deg 1.421 r_mcangle_it 1.302 r_mcbond_it 0.828 r_nbtor_refined 0.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.832 r_dihedral_angle_4_deg 19.647 r_dihedral_angle_3_deg 13.676 r_dihedral_angle_1_deg 5.599 r_scangle_it 2.984 r_scbond_it 1.896 r_angle_refined_deg 1.421 r_mcangle_it 1.302 r_mcbond_it 0.828 r_nbtor_refined 0.328 r_symmetry_vdw_refined 0.26 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2423 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement BBS data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing