☰ Navigation Tabs
Crystal structure of caspase-3 with inhibitor Ac-ITAKD-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 30 mM NaN3
Crystal Properties Matthews coefficient Solvent content 2.67 53.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.226 α = 90 b = 129.226 β = 90 c = 60.642 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 2021-04-18 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 2.55 64.61 100 0.169 0.182 0.069 0.989 9.1 7.6 19040
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 2.55 2.69 100 0.706 0.762 0.282 0.798 7.6
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2H65 2.55 34.69 1.35 19014 908 99.95 0.1805 0.1774 0.2416 0.2537 38.91
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 18.486 f_angle_d 0.9456 f_chiral_restr 0.0547 f_bond_d 0.0081 f_plane_restr 0.0078
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3799 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction JDirector data collection PHASER phasing AutoProcess data reduction