☰ Navigation Tabs
Crystal structure of human caspase-1 (Glu390->Asp and Arg286->Lys) 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, 200 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3, 2 mM MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.35 47.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.164 α = 90 b = 63.164 β = 90 c = 141.544 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 CCD ADSC QUANTUM 315 Rh coated bent cylindrical mirror 2005-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL1-5 1.16 SSRL BL1-5
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 95.6 16666 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 2.17 82.7
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 2.1 20 16362 15528 834 93.82 0.214 0.18232 0.17959 0.1786 0.23632 0.2284 RANDOM 16.587
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] -0.36 -0.36 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.635 r_scangle_it 3.698 r_mcangle_it 2.983 r_scbond_it 2.448 r_mcbond_it 1.793 r_angle_refined_deg 1.001 r_nbd_refined 0.183 r_symmetry_hbond_refined 0.149 r_symmetry_vdw_refined 0.14 r_xyhbond_nbd_refined 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.635 r_scangle_it 3.698 r_mcangle_it 2.983 r_scbond_it 2.448 r_mcbond_it 1.793 r_angle_refined_deg 1.001 r_nbd_refined 0.183 r_symmetry_hbond_refined 0.149 r_symmetry_vdw_refined 0.14 r_xyhbond_nbd_refined 0.117 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 2041 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction d*TREK data scaling AMoRE phasing