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Crystal structure of SlpA domain II (aa 201-310), domain that is involved in the self-assembly and dimerization of the S-layer from Lactobacillus acidophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 Condition: 1.0 M Sodium citrate tribasic dihydrate, 0.1 M MES, pH 6.5
Protein: 10 mg/ml in 150 mM NaCl, 25 mM HEPES, pH 7.0
0.5 ul protein mixed with 0.5 ul condition
Crystal Properties Matthews coefficient Solvent content 3.65 66.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.69 α = 90 b = 137.69 β = 90 c = 51.301 γ = 120
Symmetry Space Group P 32 2 1
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 EIGER X 16M 2022-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033230 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 47.124 99.97 0.01155 1 23.76 2 32853 56.71
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.175 99.97 0.4849 0.909 1.57 2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.1 47.124 32853 1696 99.976 0.191 0.1892 0.1896 0.2221 0.2223 69.669
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] -0.753 -0.376 -0.753 2.442
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.309 r_dihedral_angle_3_deg 13.926 r_lrange_it 10.821 r_lrange_other 10.806 r_scangle_it 8.016 r_scangle_other 8.014 r_dihedral_angle_1_deg 7.587 r_mcangle_it 6.654 r_mcangle_other 6.652 r_dihedral_angle_2_deg 5.864
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.309 r_dihedral_angle_3_deg 13.926 r_lrange_it 10.821 r_lrange_other 10.806 r_scangle_it 8.016 r_scangle_other 8.014 r_dihedral_angle_1_deg 7.587 r_mcangle_it 6.654 r_mcangle_other 6.652 r_dihedral_angle_2_deg 5.864 r_scbond_it 5.68 r_scbond_other 5.678 r_mcbond_it 4.806 r_mcbond_other 4.804 r_angle_refined_deg 1.498 r_angle_other_deg 0.518 r_nbd_refined 0.223 r_symmetry_nbd_refined 0.215 r_xyhbond_nbd_refined 0.212 r_nbd_other 0.206 r_symmetry_nbd_other 0.188 r_symmetry_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.17 r_ncsr_local_group_3 0.135 r_ncsr_local_group_2 0.131 r_ncsr_local_group_1 0.125 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2495 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing