☰ Navigation Tabs
Structure of zymogen of cathepsin B1 from Schistosoma mansoni
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QSD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 Reservoir: 0.1M Ammonium Acetate, 0.1M Bis-Tris, 17% PEG 10000. Protein buffer and concentration: 5mM Sodium Acetate, pH 5.5, Cpr=5.25mg/ml. Ratio Protein: Reservoir=2:1. Cryocooled in mother liquor containing 20% ethylene glycol., VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.281 α = 76.97 b = 83.172 β = 86.6 c = 84.569 γ = 71.11
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 MARMOSAIC 225 mm CCD Double crystal monochromator with 2 sets of Rh-soated silicon and glass mirrors 2011-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.914 BESSY 14.2
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 1.95 50 78.4 0.037 25.9 2.3 78650 25.2
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 1.95 1.98 42.1 0.296 3.1 1.9
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 3QSD 1.95 38.4 95142 71614 3756 75.27 0.20195 0.20195 0.19927 0.1951 0.25245 0.2461 RANDOM 21.792
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] 0.01 0.01 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.195 r_dihedral_angle_4_deg 17.278 r_dihedral_angle_3_deg 15.521 r_dihedral_angle_1_deg 6.062 r_scangle_it 2.26 r_scbond_it 1.513 r_angle_refined_deg 1.303 r_mcangle_it 0.911 r_mcbond_it 0.565 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.195 r_dihedral_angle_4_deg 17.278 r_dihedral_angle_3_deg 15.521 r_dihedral_angle_1_deg 6.062 r_scangle_it 2.26 r_scbond_it 1.513 r_angle_refined_deg 1.303 r_mcangle_it 0.911 r_mcbond_it 0.565 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.227 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9797 Nucleic Acid Atoms Solvent Atoms 519 Heterogen Atoms 24
Software Software Software Name Purpose MarDB data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling