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Compound 8 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 3.53 65.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.762 α = 90 b = 101.762 β = 90 c = 321.897 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 EIGER2 X 16M 2021-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03320 PETRA III, DESY P11
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 2.7 48.51 100 0.142 0.146 0.034 0.999 17.5 17.8 51597
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 2.7 2.78 100 1.513 1.556 0.365 0.903 18.2
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 2.7 48.56 48928 2566 99.93 0.19436 0.19223 0.1939 0.2347 0.2301 RANDOM 72.585
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] 3.11 1.55 3.11 -10.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.057 r_dihedral_angle_4_deg 23.661 r_dihedral_angle_3_deg 17.604 r_long_range_B_other 12.131 r_long_range_B_refined 12.124 r_scangle_other 10.034 r_mcangle_it 8.338 r_mcangle_other 8.338 r_dihedral_angle_1_deg 7.603 r_scbond_it 6.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.057 r_dihedral_angle_4_deg 23.661 r_dihedral_angle_3_deg 17.604 r_long_range_B_other 12.131 r_long_range_B_refined 12.124 r_scangle_other 10.034 r_mcangle_it 8.338 r_mcangle_other 8.338 r_dihedral_angle_1_deg 7.603 r_scbond_it 6.796 r_scbond_other 6.795 r_mcbond_it 5.825 r_mcbond_other 5.822 r_angle_refined_deg 1.5 r_angle_other_deg 1.268 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 8001 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 42
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing