☰ Navigation Tabs
Contact-dependent inhibition system from Escherichia coli NC101 - ternary CdiA/CdiI/EF-Tu complex (trypsin-modified)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I4Q 5I4Q,1ERC experimental model PDB 1ERC 5I4Q,1ERC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 0.05 M KCl 0.1 M HEPES pH=7.0, 1.0 M ammonium sulfate, cryo 3.0 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.41 63.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.395 α = 90 b = 128.354 β = 109.58 c = 100.358 γ = 90
Symmetry Space Group P 1 21 1
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 315r mirror 2014-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
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 3.3 30 99.3 0.118 10.6 3.7 26374 -3 63.3
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 3.3 3.36 98.2 0.959 1.5 3.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5I4Q,1ERC 3.3 30 24766 1008 96.41 0.24399 0.24299 0.26778 0.2344 RANDOM 115.53
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] 0.35 3.4 4.69 -5.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.118 r_dihedral_angle_4_deg 16.133 r_dihedral_angle_3_deg 14.271 r_long_range_B_refined 7.857 r_long_range_B_other 7.857 r_dihedral_angle_1_deg 5.765 r_scangle_other 3.956 r_mcangle_it 3.392 r_mcangle_other 3.392 r_scbond_it 2.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.118 r_dihedral_angle_4_deg 16.133 r_dihedral_angle_3_deg 14.271 r_long_range_B_refined 7.857 r_long_range_B_other 7.857 r_dihedral_angle_1_deg 5.765 r_scangle_other 3.956 r_mcangle_it 3.392 r_mcangle_other 3.392 r_scbond_it 2.336 r_scbond_other 2.336 r_mcbond_it 1.982 r_mcbond_other 1.981 r_angle_refined_deg 1.445 r_angle_other_deg 1.089 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.003 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8885 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing