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Crystal structure of human caspase-1 (Arg286->Ala, Glu390->Ala) 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, 100 MM LI2SO4, 25% PEG 2000 MME, 10 MM DTT, 3 MM NAN3, 2 MM MGCL2, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.37 48.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.245 α = 90 b = 63.245 β = 90 c = 142.241 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 2005-04-20 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 1.9 20 91.7 23540 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 1.9 1.97 96.3
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 1.9 20 23540 20408 1109 91.4 0.22476 0.225 0.223 0.2218 0.249 0.2499 RANDOM 19.14
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] -0.36 -0.36 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.263 r_scangle_it 2.329 r_mcangle_it 2.18 r_scbond_it 1.484 r_mcbond_it 1.307 r_angle_refined_deg 0.899 r_nbd_refined 0.162 r_symmetry_vdw_refined 0.126 r_xyhbond_nbd_refined 0.088 r_symmetry_hbond_refined 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.263 r_scangle_it 2.329 r_mcangle_it 2.18 r_scbond_it 1.484 r_mcbond_it 1.307 r_angle_refined_deg 0.899 r_nbd_refined 0.162 r_symmetry_vdw_refined 0.126 r_xyhbond_nbd_refined 0.088 r_symmetry_hbond_refined 0.067 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2011 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection d*TREK data reduction AMoRE phasing REFMAC refinement CrystalClear data reduction d*TREK data scaling