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CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-3 WITH A NICOTINIC ACID ALDEHYDE INHIBITOR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PAU Protein part of 1pau.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.7 293 9% PEG-6000, 100 mM citrate, 10 mM DTT, 3 mM NaN(3), pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.065 α = 90 b = 70.902 β = 129.2 c = 86.567 γ = 90
Symmetry Space Group C 1 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 293 AREA DETECTOR SIEMENS 1996-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 2.5 20 0.059 14.4 2.28 20718 18547 19.4
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) 2.5 2.59 33.3 0.249 3.24 2.25
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Protein part of 1pau.pdb 2.5 19.89 18590 16933 1657 83 0.192 0.1872 0.249 0.2365 RANDOM 27.4
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] -3.19 1.16 5.28 -2.1
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.3 c_scangle_it 3.21 c_mcangle_it 2.46 c_scbond_it 2.04 c_mcbond_it 1.44 c_angle_deg 1.4 c_improper_angle_d 1.18 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.3 c_scangle_it 3.21 c_mcangle_it 2.46 c_scbond_it 2.04 c_mcbond_it 1.44 c_angle_deg 1.4 c_improper_angle_d 1.18 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3744 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 50
Software Software Software Name Purpose CNX refinement X-GEN data reduction SAINT data scaling X-PLOR phasing