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Schistosoma mansoni Cathepsin D1 bound to Nb10C9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SmCD1 apo structure (personal communication) in silico model Other Predicted structure of Nb_10C9 generated with NanoBodyBuilder2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 PEG 3350, 0.1 M PCTP (sodium propionate, sodium cacodylate trihydrate, bis-tris propane), 0.2 M calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.3 46.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.141 α = 90 b = 181.8 β = 92.41 c = 78.854 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 293 PIXEL DECTRIS EIGER2 X 4M 2024-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE VMXi 0.7749 Diamond VMXi
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.59 90.9 100 0.699 0.194 1 6.7 12.1 61228
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.63 100 7.966 2.202 0.3 1 12.1
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 (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 2.59 90.9 59131 1900 99.73 0.17498 0.17302 0.1781 0.23408 0.2332 RANDOM 49.399
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] -1.2 0.41 0.28 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.087 r_long_range_B_refined 10.654 r_long_range_B_other 10.654 r_dihedral_angle_1_deg 8.475 r_scangle_other 7.806 r_dihedral_angle_2_deg 7.601 r_mcangle_it 6.877 r_mcangle_other 6.877 r_scbond_it 4.876 r_scbond_other 4.876
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.087 r_long_range_B_refined 10.654 r_long_range_B_other 10.654 r_dihedral_angle_1_deg 8.475 r_scangle_other 7.806 r_dihedral_angle_2_deg 7.601 r_mcangle_it 6.877 r_mcangle_other 6.877 r_scbond_it 4.876 r_scbond_other 4.876 r_mcbond_it 4.405 r_mcbond_other 4.402 r_angle_refined_deg 1.682 r_angle_other_deg 0.55 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 13273 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement DIALS data scaling xia2 data reduction PHASER phasing PDB_EXTRACT data extraction