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The Structure of Chagasin in Complex with a Cysteine Protease Clarifies the Binding Mode and Evolution of a New Inhibitor Family
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YVB 1YVB.PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 277 20% (v/v) PEG-300, 0.1 M Tris pH 8.5, 5% (w/v) PEG8000, and 10-15% (v/v) glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.00
Crystal Properties Matthews coefficient Solvent content 3.39 63.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.236 α = 90 b = 94.236 β = 90 c = 119.764 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD ADSC QUANTUM 4 MIRRORS 2003-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 47.12 96.7 0.094 0.09 12.6 6.3 27127 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.34 84 0.336 0.351 2.5 4.3
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 1YVB.PDB 2.2 47.12 25763 1361 96.75 0.18869 0.18643 0.1971 0.23153 0.2088 RANDOM 18.485
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] 0.23 0.23 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.161 r_dihedral_angle_3_deg 18.119 r_dihedral_angle_4_deg 15.995 r_dihedral_angle_1_deg 6.58 r_scangle_it 3.15 r_scbond_it 2.174 r_angle_refined_deg 1.519 r_mcangle_it 1.27 r_mcbond_it 1.013 r_angle_other_deg 0.977
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.161 r_dihedral_angle_3_deg 18.119 r_dihedral_angle_4_deg 15.995 r_dihedral_angle_1_deg 6.58 r_scangle_it 3.15 r_scbond_it 2.174 r_angle_refined_deg 1.519 r_mcangle_it 1.27 r_mcbond_it 1.013 r_angle_other_deg 0.977 r_symmetry_hbond_refined 0.317 r_symmetry_vdw_other 0.201 r_nbd_other 0.194 r_nbd_refined 0.192 r_nbtor_refined 0.178 r_mcbond_other 0.166 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.093 r_nbtor_other 0.089 r_symmetry_vdw_refined 0.03 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined 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 2735 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing ADSC data collection