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Crystal structures and Inhibition kinetics reveal a two-state catalytic mechanism with drug design implications for rhomboid proteolysis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IC8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 2.5M NaCl, 5% Glycerol, 0.1M Sodium acetate pH5, 7% DMPC/CHAPSO bicelle
Crystal Properties Matthews coefficient Solvent content 2.31 46.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.185 α = 90 b = 98.147 β = 90 c = 62.999 γ = 90
Symmetry Space Group C 2 2 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 270 2012-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.981 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 40 98.4 6.9 6.8 10370
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 2.2 2.24 74.1 0.437 1.9 6.1
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 2IC8 2.5 40 6937 384 92.3 0.21189 0.2079 0.2092 0.28384 0.2848 RANDOM 58.461
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] 6.56 -2.03 -4.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.982 r_dihedral_angle_3_deg 19.559 r_dihedral_angle_4_deg 12.402 r_long_range_B_refined 11.992 r_mcangle_it 7.231 r_dihedral_angle_1_deg 6.737 r_scbond_it 6.587 r_mcbond_it 5.013 r_angle_refined_deg 1.908 r_chiral_restr 0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.982 r_dihedral_angle_3_deg 19.559 r_dihedral_angle_4_deg 12.402 r_long_range_B_refined 11.992 r_mcangle_it 7.231 r_dihedral_angle_1_deg 6.737 r_scbond_it 6.587 r_mcbond_it 5.013 r_angle_refined_deg 1.908 r_chiral_restr 0.132 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 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 1397 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing