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New crystal structure of yeast Ddi1 aspartyl protease reveals substrate engagement mode
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I1A PDB entry 2I1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 295 0.1M phosphate-citrate, pH 4.2, 0.4M NaCl, 20% PEG 8000, 8 mg/ml protein, 1:1 uL drop
Crystal Properties Matthews coefficient Solvent content 2.22 44.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.515 α = 90 b = 50.051 β = 90 c = 131.562 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2008-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.9789 CHESS A1
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 1.8 50.06 96.3 0.036 25.3 4.2 25235
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 1.8 1.9 79.4 0.127 7 2.6
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 2I1A 1.8 50 23898 1285 96.07 0.18438 0.18287 0.186 0.21305 0.2162 RANDOM 37.613
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] 1.1 -1.4 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.76 r_dihedral_angle_3_deg 13.684 r_dihedral_angle_4_deg 11.246 r_dihedral_angle_1_deg 6.273 r_long_range_B_refined 4.408 r_mcangle_it 1.653 r_angle_refined_deg 1.478 r_scbond_it 1.401 r_mcbond_it 1.012 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.76 r_dihedral_angle_3_deg 13.684 r_dihedral_angle_4_deg 11.246 r_dihedral_angle_1_deg 6.273 r_long_range_B_refined 4.408 r_mcangle_it 1.653 r_angle_refined_deg 1.478 r_scbond_it 1.401 r_mcbond_it 1.012 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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_it r_scangle_other 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 2003 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction PDB_EXTRACT data extraction SCALA data scaling PHASER phasing