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Procaspase-1 zymogen domain crystal structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RWX PDB entry 1RWX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 277 0.2 M MgCl2 20% PEG 3350, pH 7.5, EVAPORATION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.36 47.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.1 α = 105.95 b = 58.004 β = 119.6 c = 60.12 γ = 92.77
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 mirrors 2007-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9779 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.05 20 97 0.058 11.2 3.1 38407 37223
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.12 87.4 0.414 1.9
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1RWX 2.05 20 38566 35359 1861 96.61 0.204 0.204 0.2 0.2119 0.263 RANDOM 36.783
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] -0.13 2.51 0.5 3.46 3.81 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.087 r_dihedral_angle_3_deg 17.207 r_dihedral_angle_4_deg 16.691 r_dihedral_angle_1_deg 6.823 r_scangle_it 5.084 r_mcangle_it 4.883 r_mcbond_it 4.02 r_scbond_it 3.67 r_angle_refined_deg 1.406 r_angle_other_deg 0.803
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.087 r_dihedral_angle_3_deg 17.207 r_dihedral_angle_4_deg 16.691 r_dihedral_angle_1_deg 6.823 r_scangle_it 5.084 r_mcangle_it 4.883 r_mcbond_it 4.02 r_scbond_it 3.67 r_angle_refined_deg 1.406 r_angle_other_deg 0.803 r_mcbond_other 0.714 r_symmetry_vdw_refined 0.278 r_nbd_refined 0.213 r_symmetry_vdw_other 0.211 r_nbd_other 0.187 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.174 r_symmetry_hbond_refined 0.119 r_nbtor_other 0.085 r_chiral_restr 0.08 r_metal_ion_refined 0.071 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other 0.001 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4286 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling PHASER phasing