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Crystal Structure of M- and C-Domains of the shaft pilin LrpA from Ligilactobacillus ruminis - iodide derivative
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 295 0.1 M sodium acetate pH 4.6, 25% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.33 47.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.903 α = 90 b = 50.898 β = 90 c = 125.623 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 PIXEL DECTRIS PILATUS 6M 2019-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.54980 ELETTRA 11.2C
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 1.905 39.58 97.6 0.129 0.13 0.018 0.999 24.2 48.4 21167
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 1.905 1.945 85.5 0.97 0.141 0.969 4.8 45.5
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 1.91 39.58 20115 1052 97.35 0.1811 0.17949 0.1894 0.21149 0.2155 RANDOM 20.742
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] -0.56 0.08 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.917 r_dihedral_angle_1_deg 7.022 r_long_range_B_refined 5.812 r_long_range_B_other 5.811 r_dihedral_angle_2_deg 4.748 r_scangle_other 4.272 r_scbond_it 2.617 r_scbond_other 2.616 r_mcangle_it 1.961 r_mcangle_other 1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.917 r_dihedral_angle_1_deg 7.022 r_long_range_B_refined 5.812 r_long_range_B_other 5.811 r_dihedral_angle_2_deg 4.748 r_scangle_other 4.272 r_scbond_it 2.617 r_scbond_other 2.616 r_mcangle_it 1.961 r_mcangle_other 1.96 r_angle_refined_deg 1.433 r_mcbond_it 1.259 r_mcbond_other 1.259 r_angle_other_deg 0.466 r_chiral_restr 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 2023 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling CRANK2 phasing