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Structure of cathepsin B1 from Schistosoma mansoni in complex with CA074 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HUC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 293 0.2M Ammonium Acetate, 0.1M Na Citrate, 30% (v/w) PEG 1500, 10mM Na Acetate pH 5.5, Cpr concentration = 5 mg/ml
protein:reservoir - 1:1 , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.09 41.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.177 α = 90 b = 79.16 β = 90 c = 90.61 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 CCD ADSC QUANTUM 210r mirrors 2009-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9791 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.3 50 93.5 0.053 26.29 5.5 59635 55759 8.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.32 61.6 0.281 2.7 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1HUC 1.3 22.33 56435 52880 2805 93.57 0.11608 0.11608 0.11407 0.1197 0.15473 0.1581 RANDOM 12.333
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 0.11 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.161 r_dihedral_angle_4_deg 13.296 r_dihedral_angle_3_deg 12.012 r_sphericity_free 10.028 r_dihedral_angle_1_deg 5.967 r_sphericity_bonded 5.028 r_scangle_it 4.501 r_scbond_it 3.404 r_mcangle_it 2.679 r_rigid_bond_restr 2.033
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.161 r_dihedral_angle_4_deg 13.296 r_dihedral_angle_3_deg 12.012 r_sphericity_free 10.028 r_dihedral_angle_1_deg 5.967 r_sphericity_bonded 5.028 r_scangle_it 4.501 r_scbond_it 3.404 r_mcangle_it 2.679 r_rigid_bond_restr 2.033 r_mcbond_it 2.019 r_angle_refined_deg 1.808 r_nbtor_refined 0.318 r_symmetry_hbond_refined 0.293 r_symmetry_vdw_refined 0.275 r_nbd_refined 0.241 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.12 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1991 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 42
Software Software Software Name Purpose HKL-3000 data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling