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Crystal structure of cathepsin D from Schistosoma mansoni
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold G4VEV6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 0.1 M Tris-HCl buffer pH 7,5
0.2M Li2SO4
25% PEG3350
The crystallization drop was composed of 2 ul protein solution + 0.8 ul precipitant solution + 0.2 ul seed stock.
Crystal Properties Matthews coefficient Solvent content 2.68 54.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 202.485 α = 90 b = 202.485 β = 90 c = 104.271 γ = 120
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 PILATUS 300K 2020-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 3.2 44.852 100 0.535 0.589 0.244 0.974 9.3 11.1 13135 67.32
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 3.2 3.42 100 4.093 4.503 1.862 0.323 11.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.292 44.852 12453 601 99.37 0.27 0.2694 0.268 0.2807 0.2789 91.369
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] 1.241 0.62 1.241 -4.025
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.827 r_dihedral_angle_3_deg 14.298 r_dihedral_angle_1_deg 7.166 r_dihedral_angle_2_deg 6.825 r_lrange_it 5.246 r_mcangle_it 2.276 r_scangle_it 2.192 r_angle_refined_deg 2.022 r_mcbond_it 1.28 r_scbond_it 1.244
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.827 r_dihedral_angle_3_deg 14.298 r_dihedral_angle_1_deg 7.166 r_dihedral_angle_2_deg 6.825 r_lrange_it 5.246 r_mcangle_it 2.276 r_scangle_it 2.192 r_angle_refined_deg 2.022 r_mcbond_it 1.28 r_scbond_it 1.244 r_nbtor_refined 0.304 r_symmetry_nbd_refined 0.241 r_nbd_refined 0.201 r_ncsr_local_group_1 0.178 r_chiral_restr 0.15 r_xyhbond_nbd_refined 0.103 r_symmetry_xyhbond_nbd_refined 0.092 r_gen_planes_refined 0.014 r_bond_refined_d 0.01 r_ext_dist_refined_b 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5097 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing