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Crystal structure of an active-site ligand-free form of the human caspase-1 C285A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RWN PDB ENTRY 1RWN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 278 0.1 M HEPES, 2 M (NH4)2SO4, 25 mM DTT. 0.01% Triton-X was added to the drop to prevent the crystals from attaching themselves to the cover slips., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.93 57.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.782 α = 90 b = 71.782 β = 90 c = 118.451 γ = 120
Symmetry Space Group P 32 2 1
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 2003-05-27 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 2.6 20 99.6 0.107 11308
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 2.6 2.69 100 0.328
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 ENTRY 1RWN 2.6 20 10163 1100 99.59 0.23486 0.23062 0.2278 0.27273 0.267 RANDOM 51.343
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] 3.31 1.65 3.31 -4.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.476 r_mcangle_it 4.146 r_scangle_it 3.503 r_mcbond_it 2.356 r_scbond_it 2.121 r_angle_refined_deg 0.979 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.132 r_symmetry_hbond_refined 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.476 r_mcangle_it 4.146 r_scangle_it 3.503 r_mcbond_it 2.356 r_scbond_it 2.121 r_angle_refined_deg 0.979 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.132 r_symmetry_hbond_refined 0.089 r_chiral_restr 0.065 r_bond_refined_d 0.007 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 2030 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction d*TREK data scaling AMoRE phasing