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Crystal structure of human caspase-1 (Glu390->Asp) in complex with 3-[2-(2-benzyloxycarbonylamino-3-methyl-butyrylamino)-propionylamino]-4-oxo-pentanoic acid (z-VAD-FMK)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SC3 PDB ENTRY 1SC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 0.1 M PIPES, 200 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3, 2 mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.67 54.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.214 α = 90 b = 63.214 β = 90 c = 161.328 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE RIGAKU RAXIS IV 2005-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54
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 2 20 92 21109 1 5
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 2 2.07 98.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1SC3 2 20 21065 19985 1079 91.8 0.238 0.21212 0.21029 0.2055 0.2466 0.2403 RANDOM 26.197
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] 0.86 0.86 -1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.035 r_scangle_it 2.411 r_mcangle_it 2.394 r_scbond_it 1.472 r_mcbond_it 1.38 r_angle_refined_deg 0.888 r_nbd_refined 0.158 r_symmetry_vdw_refined 0.12 r_symmetry_hbond_refined 0.081 r_xyhbond_nbd_refined 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.035 r_scangle_it 2.411 r_mcangle_it 2.394 r_scbond_it 1.472 r_mcbond_it 1.38 r_angle_refined_deg 0.888 r_nbd_refined 0.158 r_symmetry_vdw_refined 0.12 r_symmetry_hbond_refined 0.081 r_xyhbond_nbd_refined 0.08 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2052 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction d*TREK data scaling AMoRE phasing