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Crystal structure of human caspase-1 in complex with 4-oxo-3-[2-(5-{[4-(quinoxalin-2-ylamino)-benzoylamino]-methyl}-thiophen-2-yl)-acetylamino]-pentanoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ICE PDB ID 1ICE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 278 0.1M PIPES, 200mM Li2SO4, 25% PEG2K MME, 10mM DTT, 3mM NaN3, 2mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.67 53.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.221 α = 90 b = 63.221 β = 90 c = 161.164 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 2003-01-24 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 2.7 20 97.2 0.128 9552
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 2.7 2.79 98.6 0.382
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 1ICE 2.7 20 9552 8766 437 96.34 0.20191 0.19934 0.1963 0.25437 0.2499 RANDOM 33.988
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] 1.49 1.49 -2.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.038 r_mcangle_it 3.284 r_scangle_it 3.024 r_mcbond_it 1.89 r_scbond_it 1.781 r_angle_refined_deg 1.111 r_nbd_refined 0.174 r_symmetry_vdw_refined 0.133 r_symmetry_hbond_refined 0.132 r_xyhbond_nbd_refined 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.038 r_mcangle_it 3.284 r_scangle_it 3.024 r_mcbond_it 1.89 r_scbond_it 1.781 r_angle_refined_deg 1.111 r_nbd_refined 0.174 r_symmetry_vdw_refined 0.133 r_symmetry_hbond_refined 0.132 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.06 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 2069 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction d*TREK data scaling AMoRE phasing