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Crystal Structure of the shaft pilin LrpA from Ligilactobacillus ruminis - orthorhombic form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8KB2 The crystal structure of M- and C- domains of LrpA shaft pilin from Ligilactobacillus ruminis- NaI derivative experimental model PDB 8W5B The N-domain from the full length crystal structure of LrpA shaft pilin of Ligilactobacillus ruminis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 100 mM Sodium Acetate, pH 4.5, 20% w/v Polyethylene Glycol 3000
Crystal Properties Matthews coefficient Solvent content 2.62 53.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.416 α = 90 b = 165.24 β = 90 c = 47.928 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS 6M 2020-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972423 ESRF ID23-1
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 2.3 58.46 94.4 0.139 0.148 0.052 0.997 8.1 8.1 15406
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 2.3 2.468 91.9 0.899 0.964 0.345 0.783 7.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.3 58.46 14652 753 67.45 0.21789 0.21574 0.26161 0.2852 RANDOM 43.693
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] -0.41 -0.01 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.474 r_dihedral_angle_1_deg 6.94 r_long_range_B_refined 5.239 r_long_range_B_other 5.238 r_scangle_other 3.94 r_mcangle_it 3.182 r_mcangle_other 3.182 r_dihedral_angle_2_deg 3.012 r_scbond_it 2.378 r_scbond_other 2.377
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.474 r_dihedral_angle_1_deg 6.94 r_long_range_B_refined 5.239 r_long_range_B_other 5.238 r_scangle_other 3.94 r_mcangle_it 3.182 r_mcangle_other 3.182 r_dihedral_angle_2_deg 3.012 r_scbond_it 2.378 r_scbond_other 2.377 r_mcbond_it 2.005 r_mcbond_other 2.005 r_angle_refined_deg 1.253 r_angle_other_deg 0.387 r_chiral_restr 0.049 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 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 3023 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing