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Caspase-7 in complex with DICA allosteric inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K88 PDB ENTRY 1K88
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 277 citrate, LiSO4, NaCl, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.69 66.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.097 α = 90 b = 91.097 β = 90 c = 184.465 γ = 120
Symmetry Space Group P 32 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 93 IMAGE PLATE RIGAKU RAXIS IV mirrors 2003-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 2.8 19.98 99 0.062 9.1 2.31 22245 69.4
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) 2.8 2.9 98.6 0.34 2.8 2.32 2228
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 1K88 2.8 20 21868 20738 1130 97.33 0.24635 0.24422 0.2313 0.28651 0.2746 RANDOM 61.07
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] 3.16 1.58 3.16 -4.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.523 r_mcangle_it 4.091 r_scangle_it 3.661 r_mcbond_it 2.346 r_scbond_it 2.288 r_angle_refined_deg 1.342 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.218 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.523 r_mcangle_it 4.091 r_scangle_it 3.661 r_mcbond_it 2.346 r_scbond_it 2.288 r_angle_refined_deg 1.342 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.218 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.131 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 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 3324 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling AMoRE phasing