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Crystal structure of pilus adhesin, SpaC from Lactobacillus rhamnosus GG - open conformation
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 295 0.1 M sodium sulphate, 0.1 M Bis-Tris propane pH 6.5, 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.25 62.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.045 α = 90 b = 110.023 β = 90 c = 128.344 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 2016-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97934 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.93 83.531 83.8 0.055 0.029 0.999 14.3 4 52205 28.15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 2.042 0.575 0.352 0.732 1.9 2.8
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 MOLECULAR REPLACEMENT THROUGHOUT 1.93 83.53 49612 2597 59.75 0.2086 0.2066 0.217 0.24757 0.2545 RANDOM 38.801
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] -0.06 0.77 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.837 r_dihedral_angle_4_deg 14.823 r_dihedral_angle_3_deg 13.547 r_dihedral_angle_1_deg 6.586 r_long_range_B_refined 4.741 r_long_range_B_other 4.741 r_scangle_other 3.284 r_mcangle_it 2.546 r_mcangle_other 2.546 r_scbond_it 2.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.837 r_dihedral_angle_4_deg 14.823 r_dihedral_angle_3_deg 13.547 r_dihedral_angle_1_deg 6.586 r_long_range_B_refined 4.741 r_long_range_B_other 4.741 r_scangle_other 3.284 r_mcangle_it 2.546 r_mcangle_other 2.546 r_scbond_it 2.134 r_scbond_other 2.134 r_mcbond_it 1.627 r_mcbond_other 1.627 r_angle_refined_deg 1.311 r_angle_other_deg 1.026 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 6179 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing