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Crystal structure of caspase-3 with inhibitor Ac-VDRVD-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 15% PEG 6000, 5% glycerol (v:v), 100 mM sodium citrate pH 5.3, 10 mM DTT and 3 mM NaN3
Crystal Properties Matthews coefficient Solvent content 2.59 52.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.825 α = 90 b = 129.825 β = 90 c = 60.415 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 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 1.75 64.91 95.9 0.092 0.097 0.03 0.999 16.9 10.6 56330
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 1.75 1.84 98.9 0.729 0.767 0.235 0.924 10.3
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 1.75 56.22 1.35 56310 2816 95.92 0.1685 0.1668 0.1676 0.2018 0.2019 24.96
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 20.1392 f_angle_d 0.9415 f_chiral_restr 0.0605 f_bond_d 0.0074 f_plane_restr 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3846 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction AutoProcess data reduction PHASER phasing JDirector data collection