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Cathepsin S complexed with Compound 8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MS6 pdb entry 1MS6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 100mM NaOAc, 18-35% PEG MME (500-8000), 2 M (NH4)2SO4 with or without 15% glycerol, pH 4.6, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.77 55.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.337 α = 90 b = 85.337 β = 90 c = 150.316 γ = 90
Symmetry Space Group P 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IIC Osmic focussing mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2 50 99 0.075 7.5 38017
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT pdb entry 1MS6 2 50 38011 1952 0.184 0.1837 0.217 0.2164 random 15.229
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]
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 24.9 x_angle_deg 1.3 x_improper_angle_d 0.78 x_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3364 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 66
Software Software Software Name Purpose X-PLOR refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling X-PLOR phasing CNS refinement