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Structural Basis for Reversible and Irreversible Inhibition of Human Cathepsin L by their Respective Dipeptidyl Glyoxal and Diazomethylketone Inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CS8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 298 20 mM Sodium acetate pH 5.1, 100 mM NaCl, and 1mM EDTA, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.15 42.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.318 α = 90 b = 85.318 β = 90 c = 50.018 γ = 120
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 315 2008-03-28
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 50 86 1
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1CS8 2.2 42.659 1.34 10120 485 94.89 0.1966 0.1939 0.1923 0.253 0.2509
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] -4.5343 -4.5343 9.0685
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.195 f_angle_d 1.206 f_chiral_restr 0.074 f_plane_restr 0.009 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1706 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling MOLREP phasing CNS refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling DENZO data reduction