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Compound 7 bound to procaspase-6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.1 M HEPES pH 7, 4% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.5 64.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.57 α = 90 b = 101.57 β = 90 c = 321.26 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 EIGER X 9M 2021-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12713 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.85 48.42 60.8 0.195 0.202 0.052 0.998 11.9 15.3 26346
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 3.01 4.5 0.683 0.719 0.223 0.95 10.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.86 48.42 25010 1333 60.99 0.19047 0.18891 0.1965 0.22086 0.2346 RANDOM 40.223
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] 8.17 8.17 -16.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.984 r_dihedral_angle_4_deg 19.6 r_dihedral_angle_3_deg 18.678 r_dihedral_angle_1_deg 7.808 r_long_range_B_refined 7.725 r_long_range_B_other 7.721 r_scangle_other 4.833 r_mcangle_it 4.552 r_mcangle_other 4.552 r_scbond_it 2.748
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.984 r_dihedral_angle_4_deg 19.6 r_dihedral_angle_3_deg 18.678 r_dihedral_angle_1_deg 7.808 r_long_range_B_refined 7.725 r_long_range_B_other 7.721 r_scangle_other 4.833 r_mcangle_it 4.552 r_mcangle_other 4.552 r_scbond_it 2.748 r_scbond_other 2.748 r_mcbond_it 2.67 r_mcbond_other 2.661 r_angle_refined_deg 1.379 r_angle_other_deg 1.173 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7925 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 42
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing