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Structures of Fab-Protease Complexes Reveal a Highly Specific Non-Canonical Mechanism of Inhibition.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EAX PDB ENTRY 1EAX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 16% PEG 3350, 0.23 M MgSO4, 0.4% isopropanol, 3% glycerol, 0.12 M AMSO4, vapor diffusion, hanging drop, temperature 293k, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 3.23 61.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.598 α = 90 b = 130.598 β = 90 c = 96.941 γ = 120
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 315 KOHZU: DOUBLE CRYSTAL SI(111) 2007-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.5418 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 2.1 113 100 0.087 0.094 11.7 7.3 56788 54872 2 54.04
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 2.1 2.21 100 0.863 0.932 2.2 6.9
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 1EAX 2.1 19.88 56788 51934 2774 99.7 0.162 0.161 0.1716 0.194 0.2027 RANDOM 61.253
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] -0.53 -0.27 -0.53 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.432 r_dihedral_angle_4_deg 19.438 r_dihedral_angle_3_deg 13.67 r_dihedral_angle_1_deg 6.649 r_scangle_it 3.174 r_rigid_bond_restr 2.378 r_scbond_it 2.259 r_angle_refined_deg 1.637 r_mcangle_it 1.303 r_mcbond_it 1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.432 r_dihedral_angle_4_deg 19.438 r_dihedral_angle_3_deg 13.67 r_dihedral_angle_1_deg 6.649 r_scangle_it 3.174 r_rigid_bond_restr 2.378 r_scbond_it 2.259 r_angle_refined_deg 1.637 r_mcangle_it 1.303 r_mcbond_it 1.08 r_angle_other_deg 0.918 r_symmetry_hbond_refined 0.241 r_symmetry_vdw_other 0.213 r_mcbond_other 0.209 r_nbd_other 0.202 r_nbd_refined 0.19 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.173 r_symmetry_vdw_refined 0.138 r_chiral_restr 0.098 r_nbtor_other 0.09 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5106 Nucleic Acid Atoms Solvent Atoms 461 Heterogen Atoms 29
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement StructureStudio data collection SCALA data scaling