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Crystal structure of human caspase-1 (Cys362->Ala, Cys364->Ala, Cys397->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 0.1M Pipes pH 6.0, 200 mM ammonium sulfate, 25% PEG 2000 MME, 10 mM DTT, 2 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.66 53.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.006 α = 90 b = 63.006 β = 90 c = 161.279 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 120 IMAGE PLATE RIGAKU RAXIS IV 2003-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
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 2.2 20 97.5 16802 2
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 2.28 99.7
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 2.2 20 16372 15593 829 95.24 0.21674 0.21674 0.21392 0.2113 0.27242 0.2629 RANDOM 35.929
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] 1.05 1.05 -2.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.927 r_dihedral_angle_4_deg 15.628 r_dihedral_angle_3_deg 15.555 r_dihedral_angle_1_deg 4.99 r_mcangle_it 2.744 r_scangle_it 2.462 r_mcbond_it 1.608 r_scbond_it 1.498 r_angle_refined_deg 0.952 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.927 r_dihedral_angle_4_deg 15.628 r_dihedral_angle_3_deg 15.555 r_dihedral_angle_1_deg 4.99 r_mcangle_it 2.744 r_scangle_it 2.462 r_mcbond_it 1.608 r_scbond_it 1.498 r_angle_refined_deg 0.952 r_nbtor_refined 0.295 r_nbd_refined 0.168 r_symmetry_vdw_refined 0.133 r_xyhbond_nbd_refined 0.117 r_symmetry_hbond_refined 0.113 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2097 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction d*TREK data scaling AMoRE phasing