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Crystal structure of caspase-3 with inhibitor Ac-VDKVD-CHO
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H65
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 16% PEG 6000, 5% glycerol, 100 mM sodium citrate pH 6.5, and 10 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.43 49.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.34 α = 90 b = 67.081 β = 91.137 c = 82.183 γ = 90
Symmetry Space Group P 1 21 1
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 9M 2020-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 2.11 51.96 95.5 0.094 0.111 0.058 0.996 9.1 3.5 30167
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 2.11 2.23 99.9 0.627 0.733 0.376 0.843 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2H65 2.11 41.08 1.35 30134 1497 95.43 0.1809 0.1782 0.1785 0.2368 0.2365 34.62
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.8557 f_angle_d 0.9416 f_chiral_restr 0.0666 f_bond_d 0.008 f_plane_restr 0.0048
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3822 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction AutoProcess data reduction PHASER phasing JDirector data collection