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Crystal structure of the PI3P-binding domain of Legionella SetA in complex with inositol 1,3-bisphosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 287 20% (w/v) polyacrylic acid 5,100, 0.1 M HEPES pH 7.0, and 20 mM magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.45 49.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.247 α = 90 b = 36.915 β = 111.61 c = 72.407 γ = 90
Symmetry Space Group C 1 2 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 270 2017-12-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
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 2.46 29.52 99.1 0.11 21.5 3.86 10267
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 2.46 2.55 0.437
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.46 29.52 9749 517 98.86 0.20737 0.20493 0.2169 0.25322 0.2636 RANDOM 40.111
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] 5.07 -2.59 -0.5 -1.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.731 r_long_range_B_refined 6.469 r_long_range_B_other 6.449 r_dihedral_angle_1_deg 5.989 r_scangle_other 4.202 r_mcangle_it 3.68 r_mcangle_other 3.678 r_dihedral_angle_2_deg 2.864 r_scbond_it 2.35 r_scbond_other 2.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.731 r_long_range_B_refined 6.469 r_long_range_B_other 6.449 r_dihedral_angle_1_deg 5.989 r_scangle_other 4.202 r_mcangle_it 3.68 r_mcangle_other 3.678 r_dihedral_angle_2_deg 2.864 r_scbond_it 2.35 r_scbond_other 2.349 r_mcbond_it 2.09 r_mcbond_other 2.09 r_angle_refined_deg 0.859 r_angle_other_deg 0.297 r_chiral_restr 0.038 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 1727 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHENIX phasing