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Crystal structure of SpaE basal pilin from Lactobacillus rhamnosus GG - Selenium derivative
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 0.1 M bis-tris propane pH 8.5, 0.3 M sodium formate, 30% (w/v) PEG 3350, 1 M sodium iodide, 0.1 M L-proline
Crystal Properties Matthews coefficient Solvent content 1.95 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.779 α = 90 b = 63.936 β = 90 c = 131.112 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 225 mm CCD 2016-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97868 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.712 65.556 100 0.08 0.086 0.032 0.997 19.2 7.2 38761 23.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.712 1.741 100 0.884 0.951 0.348 0.793 2.3 7.3
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 1.712 65.556 36810 1947 99.94 0.19571 0.19427 0.2088 0.22312 0.2376 RANDOM 31.362
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] 1.24 2.39 -3.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.397 r_dihedral_angle_4_deg 17.22 r_dihedral_angle_3_deg 12.734 r_dihedral_angle_1_deg 6.973 r_long_range_B_refined 5.266 r_long_range_B_other 5.182 r_scangle_other 3.392 r_mcangle_it 2.7 r_mcangle_other 2.699 r_scbond_it 2.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.397 r_dihedral_angle_4_deg 17.22 r_dihedral_angle_3_deg 12.734 r_dihedral_angle_1_deg 6.973 r_long_range_B_refined 5.266 r_long_range_B_other 5.182 r_scangle_other 3.392 r_mcangle_it 2.7 r_mcangle_other 2.699 r_scbond_it 2.303 r_scbond_other 2.302 r_angle_refined_deg 1.971 r_mcbond_it 1.777 r_mcbond_other 1.777 r_angle_other_deg 1.43 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 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 2335 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling CRANK2 phasing