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Structure of mature form 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 5.6 293 Reservoir: 0.2M Ammonium Acetate, 0.1M Sodium Citrate, 30% PEG 4000. Protein buffer and concentration: 5mM Sodium Acetate, pH 5.5, Cpr=2.5mg/ml. Ratio Protein: Reservoir=1:1. Cryocooled in mother liquor, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.143 α = 90 b = 79.173 β = 90 c = 90.483 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 2008-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.978 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 89.9 0.077 33.7 7.3 66361 59658 13.5
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 49.3 0.438 4 5.7
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 1.3 19.79 56496 50812 2711 89.95 0.13936 0.13936 0.1374 0.1366 0.17667 0.1754 RANDOM 11.512
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] 0.52 -0.39 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.279 r_dihedral_angle_4_deg 13.942 r_dihedral_angle_3_deg 11.924 r_sphericity_free 6.247 r_dihedral_angle_1_deg 5.799 r_sphericity_bonded 4.449 r_scangle_it 3.857 r_scbond_it 2.718 r_mcangle_it 2.096 r_rigid_bond_restr 1.537
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.279 r_dihedral_angle_4_deg 13.942 r_dihedral_angle_3_deg 11.924 r_sphericity_free 6.247 r_dihedral_angle_1_deg 5.799 r_sphericity_bonded 4.449 r_scangle_it 3.857 r_scbond_it 2.718 r_mcangle_it 2.096 r_rigid_bond_restr 1.537 r_mcbond_it 1.473 r_angle_refined_deg 1.437 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.204 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.191 r_symmetry_hbond_refined 0.15 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 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 1993 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 5
Software Software Software Name Purpose HKL-3000 data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling