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Compound 10 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 64.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.481 α = 90 b = 101.481 β = 90 c = 321.539 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 PILATUS3 6M 2020-12-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.000050 ALS 5.0.2
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 2.86 45.86 100 0.256 0.264 0.067 0.997 10.6 15.5 43163
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 2.86 2.97 100 1.73 1.788 0.449 0.834 15.8
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 45.9 40864 2209 99.95 0.2023 0.19999 0.2021 0.24641 0.2449 RANDOM 64.161
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] 2.62 1.31 2.62 -8.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.166 r_dihedral_angle_4_deg 21.937 r_dihedral_angle_3_deg 18.221 r_long_range_B_refined 10.583 r_long_range_B_other 10.576 r_scangle_other 7.893 r_dihedral_angle_1_deg 7.354 r_mcangle_other 6.984 r_mcangle_it 6.983 r_scbond_it 5.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.166 r_dihedral_angle_4_deg 21.937 r_dihedral_angle_3_deg 18.221 r_long_range_B_refined 10.583 r_long_range_B_other 10.576 r_scangle_other 7.893 r_dihedral_angle_1_deg 7.354 r_mcangle_other 6.984 r_mcangle_it 6.983 r_scbond_it 5.069 r_scbond_other 5.069 r_mcbond_it 4.519 r_mcbond_other 4.514 r_angle_refined_deg 1.425 r_angle_other_deg 1.218 r_chiral_restr 0.057 r_bond_refined_d 0.007 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 134 Heterogen Atoms 42
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing