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Structure of Cathepsin S in complex with Compound 20b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other unpublished isomorphous structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 277 0.10 M sodium citrate pH 4.8, 0.2 M ammonium sulfate, 29% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.79 55.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.84 α = 90 b = 85.84 β = 90 c = 151.9 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 PIXEL DECTRIS PILATUS 6M-F 2017-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 1.3 30 93.6 0.063 0.022 0.999 16.6 8 129490
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.37 96.4 0.707 0.256 0.748 2.8 7.3
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-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE unpublished isomorphous structure 1.3 29.779 129488 6484 92.89 0.098 0.0966 0.0967 0.1306 0.13 15.978
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] 0.006 0.006 -0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.365 r_dihedral_angle_4_deg 16.031 r_dihedral_angle_1_deg 14.145 r_dihedral_angle_3_deg 11.846 r_dihedral_angle_other_3_deg 10.551 r_lrange_it 4.882 r_lrange_other 4.063 r_rigid_bond_restr 3.999 r_scbond_it 3.317 r_scbond_other 3.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.365 r_dihedral_angle_4_deg 16.031 r_dihedral_angle_1_deg 14.145 r_dihedral_angle_3_deg 11.846 r_dihedral_angle_other_3_deg 10.551 r_lrange_it 4.882 r_lrange_other 4.063 r_rigid_bond_restr 3.999 r_scbond_it 3.317 r_scbond_other 3.317 r_scangle_it 3.288 r_scangle_other 3.288 r_angle_refined_deg 2.18 r_mcangle_it 1.706 r_mcangle_other 1.706 r_angle_other_deg 1.646 r_mcbond_it 1.419 r_mcbond_other 1.418 r_symmetry_nbd_refined 0.268 r_nbd_other 0.263 r_chiral_restr 0.252 r_nbd_refined 0.224 r_symmetry_xyhbond_nbd_refined 0.221 r_xyhbond_nbd_refined 0.2 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.185 r_symmetry_nbtor_other 0.093 r_symmetry_xyhbond_nbd_other 0.076 r_bond_refined_d 0.018 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3428 Nucleic Acid Atoms Solvent Atoms 878 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing