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Crystal structure of S-layer protein SlpA from Lactobacillus acidophilus, domain I, Co-crystallization with HgCl2, Mutation Ser146Cys, (aa 32-198)
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;
JCSG+ screen condition 41 (0.2 M Sodium chloride, 0.1 M Sodium/potassium phosphate, pH 6.2, 50 % v/v PEG 200) with protein end concentration of 10 mg/mL corresponding to 50% of protein solution in the 1.0 uL drop and co-crystallization with 0.1 ul 2mM HgCl2
Crystal Properties Matthews coefficient Solvent content 3 59.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.36 α = 90 b = 85.36 β = 90 c = 191.965 γ = 120
Symmetry Space Group P 65 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-F 2018-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97625 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 2.15 48.38 99.9 0.041 0.045 0.018 0.999 25 10.4 23300
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 2.15 2.22 0.859 0.947 0.395 0.891 10.6
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 SAD FREE R-VALUE 2.153 48.38 23231 1153 99.91 0.221 0.2189 0.2164 0.2663 0.2626 65.442
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] 1.531 0.765 1.531 -4.966
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.53 r_dihedral_angle_other_3_deg 18.248 r_dihedral_angle_3_deg 14.962 r_lrange_other 10.921 r_lrange_it 10.914 r_scangle_it 8.866 r_scangle_other 8.863 r_mcangle_it 7.462 r_mcangle_other 7.461 r_dihedral_angle_1_deg 6.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.53 r_dihedral_angle_other_3_deg 18.248 r_dihedral_angle_3_deg 14.962 r_lrange_other 10.921 r_lrange_it 10.914 r_scangle_it 8.866 r_scangle_other 8.863 r_mcangle_it 7.462 r_mcangle_other 7.461 r_dihedral_angle_1_deg 6.662 r_scbond_it 6.658 r_scbond_other 6.635 r_mcbond_it 5.602 r_mcbond_other 5.585 r_angle_refined_deg 1.591 r_angle_other_deg 1.329 r_symmetry_xyhbond_nbd_refined 0.3 r_nbd_refined 0.211 r_symmetry_nbd_other 0.171 r_xyhbond_nbd_refined 0.156 r_nbtor_refined 0.15 r_nbd_other 0.142 r_symmetry_nbd_refined 0.121 r_ncsr_local_group_1 0.12 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2232 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling AutoSol phasing ARP/wARP model building