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Crystal structure of S-layer protein SlpA from Lactobacillus acidophilus, domain III (aa 309-444)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QEH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 Protein stock solution of 20 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl;
Index screen condition A9 (0.1 M BIS-TRIS pH 5.5, 3.0 M Sodium chloride) with protein end concentration of 10 mg/mL corresponding to 50% of protein solution in the 1.0 uL drop
Crystal Properties Matthews coefficient Solvent content 3.04 59.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.628 α = 90 b = 43.943 β = 98.824 c = 42.488 γ = 90
Symmetry Space Group C 1 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 EIGER2 X 16M 2019-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.25430 PETRA III, DESY P11
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 1.65 41.99 99.4 0.074 0.102 0.07 0.985 11.3 3.2 22102
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 1.65 1.68 0.15 0.206 0.141 0.951 3
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7QEH 1.65 41.99 22101 1143 99.321 0.16 0.1585 0.1836 0.2105 16.567
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] 0.134 -0.092 0.609 -0.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.61 r_dihedral_angle_3_deg 11.856 r_dihedral_angle_4_deg 9.205 r_dihedral_angle_1_deg 7.026 r_lrange_it 5.84 r_lrange_other 5.608 r_scangle_it 4.855 r_scangle_other 4.852 r_scbond_it 3.119 r_scbond_other 3.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.61 r_dihedral_angle_3_deg 11.856 r_dihedral_angle_4_deg 9.205 r_dihedral_angle_1_deg 7.026 r_lrange_it 5.84 r_lrange_other 5.608 r_scangle_it 4.855 r_scangle_other 4.852 r_scbond_it 3.119 r_scbond_other 3.116 r_mcangle_other 2.284 r_mcangle_it 2.279 r_angle_refined_deg 1.908 r_mcbond_it 1.54 r_mcbond_other 1.49 r_angle_other_deg 1.457 r_nbd_refined 0.214 r_symmetry_xyhbond_nbd_refined 0.21 r_xyhbond_nbd_refined 0.206 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.175 r_nbd_other 0.16 r_symmetry_nbd_refined 0.151 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1081 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building