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Crystal structure of S-layer protein SlpA from Lactobacillus amylovorus, domain I (aa 48-213)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QLE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Crystallization condition 0.1 M MES, 40 % v/v MPD, 5 % w/v PEG 8000
Protein solution 20 mg/ml in 20 mM HEPES pH 8.0, 100 mM NaCl
Setup 0.5 ul crystallization condition + 0.5 ul protein solution
Crystal Properties Matthews coefficient Solvent content 2.82 56.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.543 α = 90 b = 91.756 β = 90 c = 93.616 γ = 90
Symmetry Space Group P 21 21 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 2020-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.94290 ELETTRA 11.2C
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 2.3 43.79 99.02 0.05662 0.999 19.32 6.3 19468 45.72
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 2.3 2.382 0.4732 0.959 4.17
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7QLE 2.3 43.79 1.34 19426 1065 99.04 0.2262 0.2231 0.2831 0.2648 55.81
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.9061 f_angle_d 0.5316 f_chiral_restr 0.046 f_plane_restr 0.0032 f_bond_d 0.0029
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2456 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building