☰ Navigation Tabs
Cathepsin B1 from Schistosoma mansoni in complex with gallinamide analog 1
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 3350, streak seeding
Crystal Properties Matthews coefficient Solvent content 2.08 40.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.081 α = 90 b = 79.031 β = 90 c = 90.584 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 2018-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918 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 1.6 50 99.4 0.115 0.126 0.997 10.65 5.9 32051
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 1.6 1.7 96.5 0.9440000000000001 1.11 0.48200000000000004
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 1.6 45.292 32019 1601 99.392 0.161 0.1597 0.1714 0.1937 0.1979 17.476
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] -0.135 0.28 -0.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.944 r_dihedral_angle_4_deg 15.199 r_dihedral_angle_3_deg 12.936 r_dihedral_angle_other_3_deg 11.228 r_dihedral_angle_1_deg 6.644 r_lrange_it 5.214 r_lrange_other 5.117 r_scangle_it 4.292 r_scangle_other 4.29 r_scbond_it 2.781
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.944 r_dihedral_angle_4_deg 15.199 r_dihedral_angle_3_deg 12.936 r_dihedral_angle_other_3_deg 11.228 r_dihedral_angle_1_deg 6.644 r_lrange_it 5.214 r_lrange_other 5.117 r_scangle_it 4.292 r_scangle_other 4.29 r_scbond_it 2.781 r_scbond_other 2.78 r_mcangle_other 2.124 r_mcangle_it 2.122 r_angle_refined_deg 1.703 r_angle_other_deg 1.485 r_mcbond_it 1.431 r_mcbond_other 1.423 r_symmetry_xyhbond_nbd_other 0.211 r_symmetry_xyhbond_nbd_refined 0.205 r_nbd_refined 0.203 r_nbd_other 0.193 r_symmetry_nbd_other 0.186 r_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.171 r_symmetry_nbd_refined 0.144 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.081 r_metal_ion_refined 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1995 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction MOLREP phasing