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Crystal structure of S-layer protein SlpX from Lactobacillus acidophilus, domain III (aa 363-499)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8ALU 8ALU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 Protein stock solution of 10 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl;
Wizard 1/2 screen condition 66 (20 % w/v PEG 3000, 200 mM Ca(OAc)2, 100 mM Tris base/HCl pH 7.0) with protein end concentration of 5 mg/mL corresponding to 50% of protein solution in the 1.0 uL drop
Crystal Properties Matthews coefficient Solvent content 5.3 76.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.174 α = 90 b = 133.174 β = 90 c = 70.572 γ = 120
Symmetry Space Group P 62 2 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 2018-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0332 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 2.4 48.432 100 0.198 0.209 0.065 0.997 10.1 19.1 14935
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 2.4 2.49 1.516 1.596 0.496 0.844 19.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 8ALU 2.4 48.432 14914 766 99.966 0.179 0.1779 0.1846 0.205 0.2091 46.79
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] -3.069 -1.534 -3.069 9.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.375 r_lrange_it 16.475 r_lrange_other 16.469 r_dihedral_angle_4_deg 14.794 r_dihedral_angle_3_deg 14.677 r_scangle_it 13.869 r_scangle_other 13.862 r_scbond_it 11.134 r_scbond_other 11.125 r_dihedral_angle_1_deg 8.658
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.375 r_lrange_it 16.475 r_lrange_other 16.469 r_dihedral_angle_4_deg 14.794 r_dihedral_angle_3_deg 14.677 r_scangle_it 13.869 r_scangle_other 13.862 r_scbond_it 11.134 r_scbond_other 11.125 r_dihedral_angle_1_deg 8.658 r_mcangle_other 5.21 r_mcangle_it 5.181 r_mcbond_it 3.748 r_mcbond_other 3.615 r_angle_refined_deg 1.777 r_angle_other_deg 1.33 r_symmetry_nbd_refined 0.238 r_xyhbond_nbd_refined 0.222 r_nbd_other 0.212 r_symmetry_metal_ion_refined 0.212 r_nbd_refined 0.189 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_other 0.167 r_symmetry_xyhbond_nbd_refined 0.135 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.073 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1143 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building