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Human cathepsin-C in complex with cyclopropyl peptidyl nitrile inhibitor 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other in-house structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 291 20.0 % (w/v) PEG 6000
0.1 M sodium citrate pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.79 55.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.69 α = 90 b = 87.77 β = 90 c = 115.03 γ = 90
Symmetry Space Group I 2 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 CCD MARMOSAIC 225 mm CCD 2009-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.03796 MAX II I911-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.898 28.026 97.2 0.05 18.4 3.7 34042
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.898 1.95 96 0.394 3.4
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT in-house structure 1.898 28.026 34042 1684 97.18 0.149 0.147 0.1858 0.1738 27.472
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] 0.39 1.623 -2.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.483 r_dihedral_angle_4_deg 23.378 r_dihedral_angle_3_deg 13.309 r_dihedral_angle_1_deg 9.377 r_lrange_it 5.593 r_lrange_other 5.593 r_scangle_it 2.735 r_scangle_other 2.735 r_mcangle_it 2.474 r_mcangle_other 2.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.483 r_dihedral_angle_4_deg 23.378 r_dihedral_angle_3_deg 13.309 r_dihedral_angle_1_deg 9.377 r_lrange_it 5.593 r_lrange_other 5.593 r_scangle_it 2.735 r_scangle_other 2.735 r_mcangle_it 2.474 r_mcangle_other 2.474 r_angle_refined_deg 1.843 r_scbond_it 1.728 r_scbond_other 1.728 r_mcbond_it 1.581 r_mcbond_other 1.581 r_angle_other_deg 1.451 r_symmetry_nbd_refined 0.299 r_nbd_other 0.243 r_nbd_refined 0.212 r_symmetry_xyhbond_nbd_refined 0.197 r_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.184 r_symmetry_nbd_other 0.182 r_symmetry_xyhbond_nbd_other 0.132 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2760 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing