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Structure of Cathepsin S in complex with Compound 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other unpublished isomorphous structure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 6.8 285 54% v/v tacsimate pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.77 55.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.689 α = 90 b = 118.689 β = 90 c = 205.586 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 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 2.05 30 98.7 0.135 0.066 0.99 7.4 3.9 34644
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 2.05 2.16 99.4 0.663 0.32 0.632 2.5 4
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R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE unpublished isomorphous structure 2.05 29.691 34643 1708 98.089 0.144 0.1415 0.1519 0.1877 0.1936 31.859
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] 0.301 0.15 0.301 -0.975
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.111 r_dihedral_angle_4_deg 17.752 r_dihedral_angle_3_deg 14.491 r_dihedral_angle_1_deg 6.793 r_lrange_it 6.682 r_lrange_other 6.588 r_scangle_it 3.603 r_scangle_other 3.602 r_scbond_it 2.288 r_scbond_other 2.287
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.111 r_dihedral_angle_4_deg 17.752 r_dihedral_angle_3_deg 14.491 r_dihedral_angle_1_deg 6.793 r_lrange_it 6.682 r_lrange_other 6.588 r_scangle_it 3.603 r_scangle_other 3.602 r_scbond_it 2.288 r_scbond_other 2.287 r_mcangle_it 1.997 r_mcangle_other 1.996 r_angle_refined_deg 1.73 r_angle_other_deg 1.453 r_mcbond_it 1.327 r_mcbond_other 1.302 r_symmetry_xyhbond_nbd_refined 0.379 r_symmetry_nbd_refined 0.248 r_nbd_other 0.217 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.193 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.177 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3448 Nucleic Acid Atoms Solvent Atoms 444 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing