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Crystal structure of human caspase-1 (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, 350 MM LI2SO4, 20% 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 2.68 54.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.27 α = 90 b = 63.27 β = 90 c = 160.933 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 2003-10-10 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 2.1 20 99.9 19871 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 2.1 2.18 99.9
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 2.1 20 19871 18692 1009 99.1 0.22843 0.228 0.227 0.2218 0.258 0.254 RANDOM 32.32
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] 1.42 1.42 -2.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.524 r_mcangle_it 1.969 r_scangle_it 1.654 r_mcbond_it 1.096 r_scbond_it 1.014 r_angle_refined_deg 0.822 r_nbd_refined 0.145 r_symmetry_vdw_refined 0.104 r_symmetry_hbond_refined 0.077 r_xyhbond_nbd_refined 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 4.524 r_mcangle_it 1.969 r_scangle_it 1.654 r_mcbond_it 1.096 r_scbond_it 1.014 r_angle_refined_deg 0.822 r_nbd_refined 0.145 r_symmetry_vdw_refined 0.104 r_symmetry_hbond_refined 0.077 r_xyhbond_nbd_refined 0.071 r_chiral_restr 0.051 r_bond_refined_d 0.005 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 2069 Nucleic Acid Atoms Solvent Atoms 160 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