5I4R

Contact-dependent inhibition system from Escherichia coli NC101 - ternary CdiA/CdiI/EF-Tu complex (trypsin-modified)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5I4Q5I4Q,1ERC
experimental modelPDB 1ERC5I4Q,1ERC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72770.05 M KCl 0.1 M HEPES pH=7.0, 1.0 M ammonium sulfate, cryo 3.0 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
3.4163.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.395α = 90
b = 128.354β = 109.58
c = 100.358γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirror2014-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97918APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.33099.30.11810.63.726374-363.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.33.3698.20.9591.53.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5I4Q,1ERC3.33024766100896.410.243990.242990.26778RANDOM115.53
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]
0.353.44.69-5.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.118
r_dihedral_angle_4_deg16.133
r_dihedral_angle_3_deg14.271
r_long_range_B_refined7.857
r_long_range_B_other7.857
r_dihedral_angle_1_deg5.765
r_scangle_other3.956
r_mcangle_it3.392
r_mcangle_other3.392
r_scbond_it2.336
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.118
r_dihedral_angle_4_deg16.133
r_dihedral_angle_3_deg14.271
r_long_range_B_refined7.857
r_long_range_B_other7.857
r_dihedral_angle_1_deg5.765
r_scangle_other3.956
r_mcangle_it3.392
r_mcangle_other3.392
r_scbond_it2.336
r_scbond_other2.336
r_mcbond_it1.982
r_mcbond_other1.981
r_angle_refined_deg1.445
r_angle_other_deg1.089
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.003
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 AtomsNumber
Protein Atoms8885
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing