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Crystal structure of S-layer protein SlpA from Lactobacillus acidophilus, domain II (aa 199-308)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QEC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 protein stock solution of 18.5 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; JCSG+ screen condition 1-1 (0.18 M lithium sulfate, 90 mM sodium acetate pH 4.5 and 45 % w/v PEG 400) with protein end concentration of 12.3 mg/mL corresponding to 66.67 % of protein solution in the 1.5 uL drop.
Crystal Properties Matthews coefficient Solvent content 2.48 50.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.851 α = 90 b = 55.851 β = 90 c = 63.732 γ = 120
Symmetry Space Group P 31 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 PILATUS 6M-F 2017-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 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 1.4 48.37 100 0.085 0.095 0.042 0.997 13.6 9.5 23163
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 1.4 1.42 0.85 0.953 0.427 0.821 9.1
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 7QEC 1.4 48.368 23133 1177 99.97 0.172 0.1702 0.1702 0.1981 0.1985 19.088
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] -0.361 -0.181 -0.361 1.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.481 r_dihedral_angle_4_deg 18.184 r_dihedral_angle_3_deg 10.405 r_dihedral_angle_1_deg 6.325 r_lrange_it 5.608 r_lrange_other 5.468 r_scangle_it 5.008 r_scangle_other 5.004 r_scbond_it 3.554 r_scbond_other 3.554
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.481 r_dihedral_angle_4_deg 18.184 r_dihedral_angle_3_deg 10.405 r_dihedral_angle_1_deg 6.325 r_lrange_it 5.608 r_lrange_other 5.468 r_scangle_it 5.008 r_scangle_other 5.004 r_scbond_it 3.554 r_scbond_other 3.554 r_mcangle_other 2.472 r_mcangle_it 2.468 r_angle_refined_deg 2.032 r_mcbond_it 1.725 r_mcbond_other 1.643 r_angle_other_deg 1.547 r_symmetry_nbd_refined 0.273 r_nbd_other 0.237 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.19 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.142 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 765 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building