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Crystal Structure of M- and C-Domains 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 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 2.32 47.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.825 α = 90 b = 50.853 β = 90 c = 125.488 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 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 1.2 39.71 99.6 0.096 0.102 0.034 0.996 12.8 8.6 84143
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 1.2 1.223 94.6 0.779 0.834 0.292 0.888 4.6 7.7
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 1.2 39.71 79877 4250 99.58 0.16956 0.16859 0.1718 0.18761 0.1905 RANDOM 8.752
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] -1.24 1.35 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.74 r_dihedral_angle_2_deg 9.448 r_dihedral_angle_1_deg 6.653 r_rigid_bond_restr 5.157 r_long_range_B_refined 1.683 r_angle_refined_deg 1.657 r_long_range_B_other 1.619 r_scangle_other 1.298 r_scbond_it 0.993 r_scbond_other 0.993
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.74 r_dihedral_angle_2_deg 9.448 r_dihedral_angle_1_deg 6.653 r_rigid_bond_restr 5.157 r_long_range_B_refined 1.683 r_angle_refined_deg 1.657 r_long_range_B_other 1.619 r_scangle_other 1.298 r_scbond_it 0.993 r_scbond_other 0.993 r_mcangle_it 0.928 r_mcangle_other 0.928 r_mcbond_it 0.649 r_mcbond_other 0.646 r_angle_other_deg 0.594 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2019 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing