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Schistosoma mansoni Phosphodiesterase 4A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SL4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 277 14-16% (w/v) PEG 3350, 0.4 M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 3.21 61.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.55 α = 90 b = 81.55 β = 90 c = 255.87 γ = 120
Symmetry Space Group P 31 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 PIXEL DECTRIS PILATUS3 S 6M 2017-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97622 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.04 47.41 99.9 0.071 0.075 0.024 0.998 14.7 9.5 64004 45.45
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.09 100 1.501 1.605 0.565 0.545 1.3 8
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 FOURIER SYNTHESIS THROUGHOUT 3SL4 2.04 85.44 60884 3042 99.94 0.20049 0.19886 0.2049 0.23276 0.2358 RANDOM 58.941
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] -0.69 -0.35 -0.69 2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.627 r_dihedral_angle_4_deg 18.611 r_dihedral_angle_3_deg 17.45 r_dihedral_angle_1_deg 7.444 r_long_range_B_refined 5.659 r_long_range_B_other 5.659 r_scangle_other 4.927 r_scbond_it 3.605 r_scbond_other 3.605 r_mcangle_it 3.553
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.627 r_dihedral_angle_4_deg 18.611 r_dihedral_angle_3_deg 17.45 r_dihedral_angle_1_deg 7.444 r_long_range_B_refined 5.659 r_long_range_B_other 5.659 r_scangle_other 4.927 r_scbond_it 3.605 r_scbond_other 3.605 r_mcangle_it 3.553 r_mcangle_other 3.552 r_angle_refined_deg 2.912 r_mcbond_it 2.784 r_mcbond_other 2.782 r_angle_other_deg 1.536 r_chiral_restr 0.249 r_bond_refined_d 0.033 r_gen_planes_refined 0.014 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5235 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing