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Caspase-3 in Complex with an Inhibitory DARPin-3.4_S76R
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 = 192.9 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 99.2 0.05 12.94 3.4 62855 1.96 35.75
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 0.61 1.96 3.4
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 84.87 59674 3181 99.2 0.19313 0.19183 0.2097 0.21731 0.2319 RANDOM 55.484
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] 2.07 1.03 2.07 -3.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.342 r_dihedral_angle_4_deg 15.846 r_dihedral_angle_3_deg 13.013 r_dihedral_angle_1_deg 7.761 r_scangle_it 1.387 r_angle_refined_deg 0.941 r_scbond_it 0.831 r_mcangle_it 0.544 r_mcbond_it 0.273 r_chiral_restr 0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.342 r_dihedral_angle_4_deg 15.846 r_dihedral_angle_3_deg 13.013 r_dihedral_angle_1_deg 7.761 r_scangle_it 1.387 r_angle_refined_deg 0.941 r_scbond_it 0.831 r_mcangle_it 0.544 r_mcbond_it 0.273 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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 5608 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing