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Crystal structure of human caspase-1 in complex with 4-oxo-3-{6-[4-(quinoxalin-2-yloxy)-benzoylamino]-2-thiophen-2-yl-hexanoylamino}-butyric acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RWN PDB ID 1RWN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 278 0.1M PIPES, 88mM (NH4)2SO4, 25% PEG 2000 MME, 10mM DTT, 3mM NaN3, 2mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.71 54.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.371 α = 90 b = 63.371 β = 90 c = 162.399 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 180 IMAGE PLATE RIGAKU RAXIS IV 2003-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.85 20 98.6 0.08 29162
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.91 95.9 0.38
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 (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 ID 1RWN 1.85 20 29162 27113 1445 97.93 0.21564 0.21428 0.2134 0.24197 0.2404 RANDOM 23.925
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] 0.68 0.68 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.002 r_scangle_it 2.306 r_mcangle_it 2.289 r_scbond_it 1.421 r_mcbond_it 1.307 r_angle_refined_deg 0.868 r_nbd_refined 0.159 r_symmetry_vdw_refined 0.108 r_symmetry_hbond_refined 0.094 r_xyhbond_nbd_refined 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.002 r_scangle_it 2.306 r_mcangle_it 2.289 r_scbond_it 1.421 r_mcbond_it 1.307 r_angle_refined_deg 0.868 r_nbd_refined 0.159 r_symmetry_vdw_refined 0.108 r_symmetry_hbond_refined 0.094 r_xyhbond_nbd_refined 0.074 r_chiral_restr 0.056 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2102 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction d*TREK data scaling AMoRE phasing