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Caspase-3 in Complex with an Inhibitory DARPin-3.4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DKO PDB ENTRY 2DKO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.3 100 MM HEPES, PH 7.3 (RT), 40 % 2-METHYL-2,4-PENTANEDIOL.
Crystal Properties Matthews coefficient Solvent content 3.11 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98 α = 90 b = 98 β = 90 c = 193.6 γ = 120
Symmetry Space Group P 31 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 90 PIXEL DECTRIS PILATUS 6M 2010-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 49 99.3 0.04 15.59 3.9 63172 1.92 35.29
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 2.2 99.5 0.6 1.92 4.03
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 2DKO 2.1 49 59961 3211 99.31 0.18667 0.18499 0.2037 0.21811 0.2337 RANDOM 55.8
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] 0.53 0.26 0.53 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.806 r_dihedral_angle_4_deg 17.665 r_dihedral_angle_3_deg 13.918 r_dihedral_angle_1_deg 8.254 r_scangle_it 2.965 r_scbond_it 1.796 r_angle_refined_deg 1.192 r_mcangle_it 1.06 r_mcbond_it 0.54 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.806 r_dihedral_angle_4_deg 17.665 r_dihedral_angle_3_deg 13.918 r_dihedral_angle_1_deg 8.254 r_scangle_it 2.965 r_scbond_it 1.796 r_angle_refined_deg 1.192 r_mcangle_it 1.06 r_mcbond_it 0.54 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5606 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing