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Crystal structure of human caspase-1 with a naturally-occurring Lys319->Arg substitution 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
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 Crystals obtained by hanging-drop vapor diffusion at 4 C (277K) against a reservoir of 0.1 M PIPES pH 6.0, 75-175 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3, and 2 mM MgCl2. All crystals cryoprotected in mother liquors supplemented with 20% (v/v) glycerol for 30-90 sec and immersion in liquid nitrogen., VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.64 53.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.968 α = 90 b = 62.968 β = 90 c = 161.783 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 160 CCD ADSC QUANTUM 210 2006-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.98 ALS 5.0.1
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 1.8 20 99.9 0.055 8 7 31131
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 1.8 1.87 100 0.323 2.3
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 (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 1SC3 1.8 20 31094 29468 1567 99.93 0.19774 0.19517 0.1925 0.24671 0.2423 RANDOM 32.155
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] 1.08 1.08 -2.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.581 r_dihedral_angle_4_deg 17.082 r_dihedral_angle_3_deg 13.146 r_dihedral_angle_1_deg 5.62 r_scangle_it 4.317 r_mcangle_it 3.485 r_scbond_it 2.771 r_mcbond_it 2.339 r_angle_refined_deg 1.056 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.581 r_dihedral_angle_4_deg 17.082 r_dihedral_angle_3_deg 13.146 r_dihedral_angle_1_deg 5.62 r_scangle_it 4.317 r_mcangle_it 3.485 r_scbond_it 2.771 r_mcbond_it 2.339 r_angle_refined_deg 1.056 r_nbtor_refined 0.297 r_nbd_refined 0.179 r_symmetry_vdw_refined 0.149 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.11 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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 2099 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction d*TREK data scaling MOLREP phasing