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Crystal structure of the APSK domain of human PAPSS1 complexed with 2 APS molecules
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M7G pdb id 1M7G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 reservoir: 18-20% PEG 3350, 0.25 M calcium acetate
protein solution: 5-8 mg/ml protein, 3 mM APS, 5 mM MgCl2, 50 mM Tris pH 7.5, 50 mM KCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.28 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.19 α = 90 b = 69.03 β = 116.61 c = 150.61 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 MARMOSAIC 225 mm CCD 2004-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 0.9594 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 2.05 10 83.6 0.095 0.082 12.4 3.7 121588 101698
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) 2.05 2.1 92.8 0.301 0.24 4.36 2.5 7260
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 id 1M7G 2.05 10 101066 10107 97.47 0.223 0.217 0.2164 0.282 0.2774 RANDOM 27.759
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] 0.62 -0.02 -0.65 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.362 r_dihedral_angle_4_deg 18.209 r_dihedral_angle_3_deg 16.318 r_dihedral_angle_1_deg 5.807 r_scangle_it 2.403 r_angle_refined_deg 1.729 r_scbond_it 1.575 r_mcangle_it 1.021 r_mcbond_it 0.611 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.362 r_dihedral_angle_4_deg 18.209 r_dihedral_angle_3_deg 16.318 r_dihedral_angle_1_deg 5.807 r_scangle_it 2.403 r_angle_refined_deg 1.729 r_scbond_it 1.575 r_mcangle_it 1.021 r_mcbond_it 0.611 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.224 r_nbd_refined 0.204 r_metal_ion_refined 0.201 r_xyhbond_nbd_refined 0.19 r_symmetry_vdw_refined 0.145 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 12417 Nucleic Acid Atoms Solvent Atoms 832 Heterogen Atoms 438
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction