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crystal structure of mouse cytosolic sulfotransferase mSULT1D1 complex with PAP and p-nitrophenol, obtained by two-step soaking method
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 3.1 60.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.313 α = 90 b = 67.838 β = 105.25 c = 42.867 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 1.8 50 99.7 0.044 0.044 23.9 3.6 39743 39743
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 1.8 1.86 99.3 0.387 0.387 2.1 3.4 3966
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 26.15 37750 1990 99.65 0.18282 0.18219 0.1819 0.19451 0.1944 RANDOM 24.162
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 0.05 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.893 r_dihedral_angle_4_deg 18.602 r_dihedral_angle_3_deg 12.811 r_dihedral_angle_1_deg 5.138 r_scangle_it 2.093 r_scbond_it 1.344 r_angle_refined_deg 1.128 r_mcangle_it 0.905 r_mcbond_it 0.545 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.893 r_dihedral_angle_4_deg 18.602 r_dihedral_angle_3_deg 12.811 r_dihedral_angle_1_deg 5.138 r_scangle_it 2.093 r_scbond_it 1.344 r_angle_refined_deg 1.128 r_mcangle_it 0.905 r_mcbond_it 0.545 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.228 r_nbd_refined 0.19 r_xyhbond_nbd_refined 0.098 r_symmetry_hbond_refined 0.097 r_chiral_restr 0.079 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2423 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement BBS data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing