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crystal structure of the APSK domain of human PAPSS1 in complex with ADPMg and PAPS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OFW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 298 reservoir: 0.2-0.4mM ammonium dihydrogenphosphate
protein solution: 6 mg/ml protein, 2 mM PAPS, 2 mM ADP, 5 mM MgCl2, 50 mM Tris pH 7.5, 50 mM KCl
, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.99 38.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.4 α = 90 b = 63.32 β = 114.38 c = 61.69 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 225 mm CCD 2004-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
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 1.89 20 97.5 0.079 0.071 18.83 5.6 28560 27832
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) 1.89 2.01 94.5 0.165 0.148 9.3 5.13 4298
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 2OFW 1.9 20 27683 2766 97.14 0.192 0.187 0.1854 0.236 0.2347 RANDOM 13.1
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] -0.22 0.11 1.16 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.381 r_dihedral_angle_4_deg 15.15 r_dihedral_angle_3_deg 14.637 r_dihedral_angle_1_deg 6.03 r_scangle_it 2.967 r_scbond_it 2.021 r_angle_refined_deg 1.571 r_mcangle_it 1.26 r_mcbond_it 0.773 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.381 r_dihedral_angle_4_deg 15.15 r_dihedral_angle_3_deg 14.637 r_dihedral_angle_1_deg 6.03 r_scangle_it 2.967 r_scbond_it 2.021 r_angle_refined_deg 1.571 r_mcangle_it 1.26 r_mcbond_it 0.773 r_nbtor_refined 0.31 r_symmetry_hbond_refined 0.252 r_symmetry_vdw_refined 0.236 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.178 r_chiral_restr 0.092 r_metal_ion_refined 0.045 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3173 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 176
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction