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Structure of Cathepsin S in complex with Compound 14
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other unpublished isomorphous structure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 4.8 285 0.1 M sodium citrate pH 4.8, 0.2 M ammonium sulfate, 17% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.76 55.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.671 α = 90 b = 85.671 β = 90 c = 150.922 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 MAR scanner 345 mm plate 2014-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 2.22 19.51 99.4 0.118 0.058 0.994 10.1 3.9 28281
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 2.22 2.34 99.8 0.68 0.344 0.732 2.5 3.8
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R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE unpublished isomorphous structure 2.22 19.51 28263 1436 99.005 0.161 0.1581 0.1655 0.217 0.2201 33.279
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] 0.171 0.171 -0.341
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.126 r_dihedral_angle_4_deg 16.093 r_dihedral_angle_3_deg 14.208 r_dihedral_angle_1_deg 6.998 r_lrange_it 6.963 r_lrange_other 6.868 r_scangle_it 2.99 r_scangle_other 2.99 r_mcangle_it 2.137 r_mcangle_other 2.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.126 r_dihedral_angle_4_deg 16.093 r_dihedral_angle_3_deg 14.208 r_dihedral_angle_1_deg 6.998 r_lrange_it 6.963 r_lrange_other 6.868 r_scangle_it 2.99 r_scangle_other 2.99 r_mcangle_it 2.137 r_mcangle_other 2.137 r_scbond_other 2.037 r_scbond_it 2.034 r_angle_refined_deg 1.741 r_angle_other_deg 1.624 r_mcbond_it 1.319 r_mcbond_other 1.319 r_nbd_other 0.257 r_symmetry_nbd_refined 0.217 r_xyhbond_nbd_refined 0.203 r_symmetry_xyhbond_nbd_refined 0.201 r_nbd_refined 0.195 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.178 r_ncsr_local_group_1 0.104 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.015 r_bond_refined_d 0.013 r_bond_other_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3447 Nucleic Acid Atoms Solvent Atoms 478 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing