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Crystal Structure of M- and C-Domains of the shaft pilin LrpA from Ligilactobacillus ruminis - Triclinic form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8KB2 LrpA, Shaft Pilin-NaI derivative
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.2 M Lithium Sulphate, 0.1 M Tris pH 8.5, 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.65 53.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.334 α = 107.25 b = 47.677 β = 101.52 c = 51.72 γ = 111.78
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 0.98030 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 1.465 39.46 95.2 0.11 0.13 0.069 0.987 6.9 3.4 47229
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 1.465 1.491 92.4 0.444 0.545 0.308 0.792 2.1 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 MOLECULAR REPLACEMENT THROUGHOUT 1.47 39.46 44908 2321 95.22 0.17545 0.17464 0.1823 0.19106 0.2004 RANDOM 11.871
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] 0.66 -0.26 -0.28 -0.29 -0.15 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.756 r_dihedral_angle_2_deg 8.494 r_dihedral_angle_1_deg 6.722 r_long_range_B_refined 3.8 r_long_range_B_other 3.624 r_scangle_other 2.598 r_scbond_it 1.702 r_scbond_other 1.701 r_angle_refined_deg 1.6 r_mcangle_it 1.499
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.756 r_dihedral_angle_2_deg 8.494 r_dihedral_angle_1_deg 6.722 r_long_range_B_refined 3.8 r_long_range_B_other 3.624 r_scangle_other 2.598 r_scbond_it 1.702 r_scbond_other 1.701 r_angle_refined_deg 1.6 r_mcangle_it 1.499 r_mcangle_other 1.498 r_mcbond_it 0.993 r_mcbond_other 0.991 r_angle_other_deg 0.555 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 1976 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing