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Compound 3 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 3.49 64.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.333 α = 90 b = 101.333 β = 90 c = 321.538 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 2021-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.000000 SPring-8 BL45XU
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 2.95 45.93 99.8 0.283 0.297 0.084 0.979 5.5 9.6 39151
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 2.95 3.07 99.8 0.793 0.832 0.239 0.909 9.7
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 2.95 45.85 37016 2044 99.78 0.19724 0.19559 0.199 0.22739 0.2269 RANDOM 69.922
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] 3.05 1.53 3.05 -9.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.395 r_dihedral_angle_4_deg 22.905 r_dihedral_angle_3_deg 18.645 r_long_range_B_other 11.672 r_long_range_B_refined 11.664 r_scangle_other 9.177 r_mcangle_other 7.95 r_mcangle_it 7.949 r_dihedral_angle_1_deg 7.717 r_scbond_it 6.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.395 r_dihedral_angle_4_deg 22.905 r_dihedral_angle_3_deg 18.645 r_long_range_B_other 11.672 r_long_range_B_refined 11.664 r_scangle_other 9.177 r_mcangle_other 7.95 r_mcangle_it 7.949 r_dihedral_angle_1_deg 7.717 r_scbond_it 6.004 r_scbond_other 6.004 r_mcbond_it 5.305 r_mcbond_other 5.3 r_angle_refined_deg 1.582 r_angle_other_deg 1.248 r_chiral_restr 0.063 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 7907 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 44
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing