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Crystal structure of the NleG5-1 effector (C200A) from Escherichia coli O157:H7 str. Sakai
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2KKY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9 293 20% P3350, 0.2 M CaCl2, 2% Hexanediol, 20 mM Tris pH 9.0, 0.2 M NaCl, 0.3 M KCl2
Crystal Properties Matthews coefficient Solvent content 3.08 60.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.376 α = 90 b = 151.376 β = 90 c = 87.983 γ = 120
Symmetry Space Group P 65 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 CCD RAYONIX MX-300 2016-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) CC (Half) 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 2.55 50.01 98.9 0.046 0.046 0.021 1 36.38 6.7 19632 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.59 100 0.638 0.494 1.2 6.9
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2KKY 2.6 50.01 15593 1739 92.25 0.25015 0.24474 0.2513 0.29704 RANDOM 83.011
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] 0.02 0.01 0.02 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.248 r_long_range_B_refined 29.174 r_long_range_B_other 29.171 r_mcangle_it 23.896 r_mcangle_other 23.89 r_scangle_other 18.386 r_dihedral_angle_4_deg 16.436 r_mcbond_other 15.883 r_mcbond_it 15.88 r_dihedral_angle_3_deg 15.745
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.248 r_long_range_B_refined 29.174 r_long_range_B_other 29.171 r_mcangle_it 23.896 r_mcangle_other 23.89 r_scangle_other 18.386 r_dihedral_angle_4_deg 16.436 r_mcbond_other 15.883 r_mcbond_it 15.88 r_dihedral_angle_3_deg 15.745 r_scbond_it 12.19 r_scbond_other 12.148 r_dihedral_angle_1_deg 5.711 r_angle_refined_deg 1.344 r_angle_other_deg 0.965 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 3276 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing