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Caspase 8 bound to a covalent inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 277 2 microliters of 100 mM inhibitor stock in DMSO was added to 100 microliters of 8.4 mg/mL protein in 20 mM Tris, 100 mM DTT, pH 8.0. Protein solution was mixed with an equal volume of well solution (1.0-1.1 M Citrate, 50 mM HEPES or PIPES pH 6.5, 25 mM DTT), VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.48 50.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.598 α = 90 b = 62.598 β = 90 c = 129.389 γ = 120
Symmetry Space Group P 31 2 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 CCD ADSC QUANTUM 210 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) 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 1.8 20 95.7 27933 26732
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.85
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 (All) 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 1.8 19.94 24018 2714 95.7 0.17025 0.17025 0.16674 0.182 0.20224 0.2154 RANDOM 9.42
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] -0.25 -0.12 -0.25 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.334 r_dihedral_angle_4_deg 13.978 r_dihedral_angle_3_deg 12.108 r_dihedral_angle_1_deg 5.725 r_scangle_it 2.064 r_scbond_it 1.318 r_angle_refined_deg 1.202 r_angle_other_deg 0.85 r_mcangle_it 0.68 r_mcbond_it 0.428
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.334 r_dihedral_angle_4_deg 13.978 r_dihedral_angle_3_deg 12.108 r_dihedral_angle_1_deg 5.725 r_scangle_it 2.064 r_scbond_it 1.318 r_angle_refined_deg 1.202 r_angle_other_deg 0.85 r_mcangle_it 0.68 r_mcbond_it 0.428 r_symmetry_vdw_other 0.198 r_nbd_refined 0.191 r_nbd_other 0.181 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.123 r_symmetry_vdw_refined 0.119 r_mcbond_other 0.089 r_nbtor_other 0.081 r_symmetry_hbond_refined 0.072 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1906 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 51
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling