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Structure of cathepsin B1 from Schistosoma mansoni in complex with WRR391 inhibitor
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 6.1 293 0.14 M Ammonium Acetate, 0.07 M Sodium Citrate, 21% PEG 400
c (protein) = 3.4 mg/ml
ratio protein : reservoir : H2O = 2:0.5:0.5ul
cryocooled in mother liquor
Crystal Properties Matthews coefficient Solvent content 2.29 46.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.39 α = 90 b = 82.39 β = 90 c = 99.39 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 2016-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.541870
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 1.91 38.06 89.5 0.078 0.095 0.996 9.72 2.799 52771 31.098
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 1.91 1.95 48.7 0.799 1.128 0.4 0.68 1.438
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 4I07 1.91 38.06 51402 1367 89.47 0.1679 0.1674 0.1709 0.1863 0.1826 RANDOM 29.432
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] 8.73 8.73 -17.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.865 r_dihedral_angle_4_deg 17.341 r_dihedral_angle_3_deg 14.736 r_dihedral_angle_1_deg 6.216 r_angle_refined_deg 1.409 r_angle_other_deg 0.843 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.865 r_dihedral_angle_4_deg 17.341 r_dihedral_angle_3_deg 14.736 r_dihedral_angle_1_deg 6.216 r_angle_refined_deg 1.409 r_angle_other_deg 0.843 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5994 Nucleic Acid Atoms Solvent Atoms 443 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction MOLREP phasing XDS data reduction