☰ Navigation Tabs
Crystal structure of caspase-3 with inhibitor Ac-YKPVD-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 2.43 49.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.103 α = 90 b = 84.16 β = 90 c = 96.333 γ = 90
Symmetry Space Group P 21 21 21
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 2.73 63.38 99.9 0.134 0.145 0.054 0.997 10.4 7.1 15257
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 2.73 2.88 99.9 0.584 0.627 0.225 0.951 7.5
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 2.73 63.38 1.35 15156 737 99.43 0.1937 0.1904 0.1916 0.2535 0.2489 42.48
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 6.1443 f_angle_d 0.9442 f_chiral_restr 0.0538 f_bond_d 0.0077 f_plane_restr 0.0072
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3765 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction AutoProcess data reduction PHASER phasing JDirector data collection