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Structure of Cathepsin S in complex with Compound 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other unpublished isomorphous structure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, SITTING DROP 7.3 285 0.2 M potassium formate pH 7.3, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.26 45.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.765 α = 90 b = 92.765 β = 90 c = 182.893 γ = 120
Symmetry Space Group P 32 2 1
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 2013-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 ESRF ID29
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 2.51 28.82 99.8 0.096 0.037 0.998 11.9 6.5 31846
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 2.51 2.65 99.9 0.623 0.232 0.913 2.6 6.9
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R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE unpublished isomorphous structure 2.51 28.82 31800 1599 99.743 0.213 0.2098 0.2127 0.2802 0.2819 74.379
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] 1.776 0.888 1.776 -5.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.737 r_dihedral_angle_3_deg 18.151 r_dihedral_angle_4_deg 14.41 r_dihedral_angle_1_deg 7.031 r_lrange_it 6.523 r_lrange_other 6.513 r_mcangle_other 3.321 r_mcangle_it 3.32 r_scangle_it 3.274 r_scangle_other 3.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.737 r_dihedral_angle_3_deg 18.151 r_dihedral_angle_4_deg 14.41 r_dihedral_angle_1_deg 7.031 r_lrange_it 6.523 r_lrange_other 6.513 r_mcangle_other 3.321 r_mcangle_it 3.32 r_scangle_it 3.274 r_scangle_other 3.274 r_mcbond_it 2.109 r_mcbond_other 2.105 r_scbond_it 1.999 r_scbond_other 1.999 r_angle_refined_deg 1.546 r_angle_other_deg 1.286 r_symmetry_nbd_refined 0.288 r_symmetry_xyhbond_nbd_refined 0.254 r_nbd_other 0.245 r_xyhbond_nbd_refined 0.21 r_nbd_refined 0.206 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_other 0.11 r_ncsr_local_group_6 0.104 r_ncsr_local_group_5 0.103 r_ncsr_local_group_3 0.099 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.076 r_ncsr_local_group_2 0.07 r_ncsr_local_group_1 0.069 r_ncsr_local_group_4 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6892 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing