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Crystal structure of human tyrosylprotein sulfotransferase-2 complexed with PAP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 283.4 0.1M Tris-HCl, pH 7.0, 0.1M calcium acetate, 20 % polyethylene glycol 3000, VAPOR DIFFUSION, SITTING DROP, temperature 283.4K
Crystal Properties Matthews coefficient Solvent content 2.08 40.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.432 α = 90 b = 81.326 β = 90 c = 226.659 γ = 90
Symmetry Space Group P 2 21 21
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 ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0000 Photon Factory BL-17A
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 3.5 50 68.1 0.164 0.165 16.5 7.7 11529 11529
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 3.5 3.56 42.9 0.464 0.464 3 6.5 364
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3AP1 3.5 48.5 11066 11066 583 67.08 0.29398 0.29026 0.2852 0.3709 RANDOM 124.515
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] -0.7 0.65 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.562 r_dihedral_angle_3_deg 18.255 r_dihedral_angle_4_deg 15.259 r_dihedral_angle_1_deg 5.626 r_scangle_it 1.795 r_angle_refined_deg 1.329 r_scbond_it 0.956 r_mcangle_it 0.655 r_mcbond_it 0.331 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.562 r_dihedral_angle_3_deg 18.255 r_dihedral_angle_4_deg 15.259 r_dihedral_angle_1_deg 5.626 r_scangle_it 1.795 r_angle_refined_deg 1.329 r_scbond_it 0.956 r_mcangle_it 0.655 r_mcbond_it 0.331 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9002 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 108
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling