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Crystal structure of human Cathepsin L in complex with 2-(benzimidazol-1-yl)-N-methylacetamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7Z3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 Mature cathepsin L at a concentration of 7 mg/ml was equilibrated against 27% w/v PEG 8000, 1 mM TCEP and 0.1 M sodium acetate at pH 4.0. Crystals, which grew to final size after approximately 3 days, were transferred to a compound soaking solution containing 22% w/v PEG 8000, 1 mM TCEP and 0.1 M sodium acetate at pH 4.0 as well as 5 % v/v DMSO and 10% v/v PEG 400. For diffraction data collection, crystals were flash-frozen after manual harvesting.
Crystal Properties Matthews coefficient Solvent content 2.14 42.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.13 α = 105.304 b = 62.681 β = 93.581 c = 67.787 γ = 115.593
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 X 16M 2023-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.79 53.505 92 0.099 0.998 12.3 6.1 69753 19.41
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.82 0.746 0.703 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 1.79 53.5 1.96 69739 3510 91.89 0.162 0.1597 0.1602 0.2041 0.2043 23.78
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 f_dihedral_angle_d 16.3597 f_angle_d 0.7991 f_chiral_restr 0.0531 f_bond_d 0.0069 f_plane_restr 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6764 Nucleic Acid Atoms Solvent Atoms 560 Heterogen Atoms 143
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing