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Structure of cathepsin B1 from Schistosoma mansoni in complex with WRR286 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 0.2 M Ammonium Acetate, 0.1 M Sodium Citrate, 30% PEG 1500
c(protein)= 5 mg/ml
ratio protein:reservoir = 1:1ul
cryocooled in mother liquor
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.484 α = 90 b = 78.072 β = 91.24 c = 77.663 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 100 PIXEL DECTRIS PILATUS 6M 2016-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 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 1.55 39.04 98.9 0.061 0.073 0.998 11.81 3.313 112101 26.825
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 1.55 1.64 98.1 0.707 0.844 0.688 1.76 3.31
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 1.55 39.04 110979 1121 98.93 0.1619 0.1615 0.1731 0.2025 0.2057 RANDOM 27.176
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] -0.28 -0.76 0.15 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.575 r_dihedral_angle_4_deg 19.521 r_dihedral_angle_3_deg 12.534 r_dihedral_angle_1_deg 6.024 r_angle_refined_deg 1.604 r_angle_other_deg 0.872 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.575 r_dihedral_angle_4_deg 19.521 r_dihedral_angle_3_deg 12.534 r_dihedral_angle_1_deg 6.024 r_angle_refined_deg 1.604 r_angle_other_deg 0.872 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5994 Nucleic Acid Atoms Solvent Atoms 884 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing