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Compound 19 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, 6% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.54 65.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.94 α = 90 b = 101.94 β = 90 c = 321.98 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 XE 16M 2021-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 2.65 52.03 100 0.111 0.115 0.031 0.999 15.4 13.3 54770
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 2.65 2.73 100 0.961 0.996 0.256 0.941 14.6
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 2.65 52.08 52026 2643 99.95 0.19472 0.19283 0.1976 0.23031 0.2308 RANDOM 69.04
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 1.5 3 -9.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.101 r_dihedral_angle_4_deg 23.061 r_dihedral_angle_3_deg 18.654 r_long_range_B_other 12.125 r_long_range_B_refined 12.115 r_scangle_other 9.812 r_mcangle_other 8.005 r_mcangle_it 7.999 r_dihedral_angle_1_deg 7.871 r_scbond_it 6.574
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.101 r_dihedral_angle_4_deg 23.061 r_dihedral_angle_3_deg 18.654 r_long_range_B_other 12.125 r_long_range_B_refined 12.115 r_scangle_other 9.812 r_mcangle_other 8.005 r_mcangle_it 7.999 r_dihedral_angle_1_deg 7.871 r_scbond_it 6.574 r_scbond_other 6.571 r_mcbond_it 5.561 r_mcbond_other 5.542 r_angle_refined_deg 1.553 r_angle_other_deg 1.272 r_chiral_restr 0.069 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 7982 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 42
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing