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Crystal structure of the human caspase-1 C285A mutant after removal of malonate
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 7 274 2 M sodium malonate, VAPOR DIFFUSION, HANGING DROP, temperature 274K. Malonate-bound enzyme crystals were transferred into mother liquor composed of 0.1 M PIPES pH 6, 88 mM (NH4)2SO4, 25% PEG 2000 MME, 10 mM DTT, 3 mM NaN3 and 2 mM MgCl2, and soaked for 2 days to remove malonate.
Crystal Properties Matthews coefficient Solvent content 2.36 47.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.982 α = 90 b = 62.982 β = 90 c = 143.158 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 180 IMAGE PLATE RIGAKU RAXIS IV 2003-07-10 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 2.1 20 95.3 0.11 17527
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 2.1 2.17 78.6 0.297
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 PDB ENTRY 1RWN 2.1 20 17527 15873 833 95.31 0.22295 0.22106 0.2206 0.2584 0.2557 RANDOM 23.579
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] 0.06 0.06 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.426 r_mcangle_it 2.763 r_scangle_it 2.711 r_scbond_it 1.662 r_mcbond_it 1.598 r_angle_refined_deg 0.911 r_nbd_refined 0.161 r_symmetry_vdw_refined 0.137 r_symmetry_hbond_refined 0.095 r_xyhbond_nbd_refined 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.426 r_mcangle_it 2.763 r_scangle_it 2.711 r_scbond_it 1.662 r_mcbond_it 1.598 r_angle_refined_deg 0.911 r_nbd_refined 0.161 r_symmetry_vdw_refined 0.137 r_symmetry_hbond_refined 0.095 r_xyhbond_nbd_refined 0.091 r_chiral_restr 0.058 r_bond_refined_d 0.006 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 1956 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction d*TREK data scaling AMoRE phasing