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Cathepsin B1 from Schistosoma mansoni in complex with gallinamide A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I07
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 278.15 0.2 M ammonium acetate, 0.1 M sodium citrate, 30% PEG 1500, streak seeding
Crystal Properties Matthews coefficient Solvent content 2.09 41.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.185 α = 90 b = 79.214 β = 90 c = 90.631 γ = 90
Symmetry Space Group P 21 21 21
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 6M 2018-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.2 50 99.6 0.087 0.094 0.9990000000000001 11.79 6.6 75696
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.27 98.7 1.4040000000000001 1.524 0.489
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 1.2 45.36 75696 1511 99.55 0.135 0.1346 0.1344 0.1653 0.165 14.588
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] -0.372 -0.192 0.564
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.345 r_dihedral_angle_4_deg 13.835 r_dihedral_angle_other_3_deg 13.729 r_dihedral_angle_3_deg 11.325 r_dihedral_angle_1_deg 6.258 r_lrange_it 3.512 r_lrange_other 2.871 r_scangle_it 2.506 r_scangle_other 2.506 r_scbond_it 2.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.345 r_dihedral_angle_4_deg 13.835 r_dihedral_angle_other_3_deg 13.729 r_dihedral_angle_3_deg 11.325 r_dihedral_angle_1_deg 6.258 r_lrange_it 3.512 r_lrange_other 2.871 r_scangle_it 2.506 r_scangle_other 2.506 r_scbond_it 2.061 r_scbond_other 2.06 r_rigid_bond_restr 1.857 r_mcangle_it 1.805 r_mcangle_other 1.804 r_angle_refined_deg 1.664 r_angle_other_deg 1.481 r_mcbond_it 1.293 r_mcbond_other 1.292 r_nbd_refined 0.207 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.171 r_nbd_other 0.17 r_symmetry_xyhbond_nbd_refined 0.162 r_xyhbond_nbd_refined 0.161 r_symmetry_nbd_refined 0.1 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.069 r_metal_ion_refined 0.046 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1981 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction MOLREP phasing