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Structure of EspB-EspK complex: the non-identical twin of the PE-PPE-EspG secretion mechanism.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XXX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 0.2-1.2 M sodium malonate
0.1 M HEPES (pH 7.8)
8-14% PEG3350
Crystal Properties Matthews coefficient Solvent content 5.06 75.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.579 α = 90 b = 101.579 β = 90 c = 377.045 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2021-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.976 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.29 85.82 53.2 0.034 11.7 6.2 28129 63.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.6 0.38 1.9
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 (All) 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 4XXX 2.293 85.816 28129 1444 53.194 0.237 0.2348 0.2348 0.2786 0.2787 RANDOM 84.479
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] -0.034 -0.017 -0.034 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.903 r_dihedral_angle_4_deg 19.125 r_dihedral_angle_3_deg 17.011 r_rigid_bond_restr 8.394 r_dihedral_angle_1_deg 6.174 r_angle_refined_deg 1.484 r_nbtor_refined 0.308 r_xyhbond_nbd_refined 0.202 r_symmetry_xyhbond_nbd_refined 0.191 r_nbd_refined 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.903 r_dihedral_angle_4_deg 19.125 r_dihedral_angle_3_deg 17.011 r_rigid_bond_restr 8.394 r_dihedral_angle_1_deg 6.174 r_angle_refined_deg 1.484 r_nbtor_refined 0.308 r_xyhbond_nbd_refined 0.202 r_symmetry_xyhbond_nbd_refined 0.191 r_nbd_refined 0.17 r_symmetry_nbd_refined 0.109 r_chiral_restr 0.095 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_mcbond_it r_mcangle_it r_scbond_it r_scangle_it r_lrange_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3892 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing