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Crystal Structure of the shaft pilin LrpA from Ligilactobacillus ruminis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8KB2 Crystal Structure of M- and C- Domains of the shaft pilin LrpA from Ligilactobacillus ruminis- iodide derivative in silico model AlphaFold N-Domain of the shaft pilin LrpA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.1 M sodium acetate pH 4.6, 15% PEG 3000, 5% polyvinylpyrrolidone K15
Crystal Properties Matthews coefficient Solvent content 3.13 60.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.391 α = 90 b = 47.391 β = 90 c = 227.411 γ = 120
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 2017-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97895 ESRF ID29
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 2.268 75.804 98.4 0.036 0.038 0.012 1 27.9 10.3 26024
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 2.268 2.307 99.7 0.819 0.86 0.264 0.888 2.5 10.5
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 MOLECULAR REPLACEMENT THROUGHOUT 2.27 75.8 24719 1305 98.34 0.22332 0.22227 0.2246 0.24019 0.2373 RANDOM 69
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] 1.93 0.97 1.93 -6.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.354 r_long_range_B_refined 9.002 r_long_range_B_other 9.002 r_dihedral_angle_1_deg 7.437 r_scangle_other 7.22 r_mcangle_it 5.895 r_mcangle_other 5.893 r_dihedral_angle_2_deg 5.354 r_scbond_it 4.876 r_scbond_other 4.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.354 r_long_range_B_refined 9.002 r_long_range_B_other 9.002 r_dihedral_angle_1_deg 7.437 r_scangle_other 7.22 r_mcangle_it 5.895 r_mcangle_other 5.893 r_dihedral_angle_2_deg 5.354 r_scbond_it 4.876 r_scbond_other 4.874 r_mcbond_it 4.425 r_mcbond_other 4.418 r_angle_refined_deg 1.264 r_angle_other_deg 0.427 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 3036 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing