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Crystal structure of EgtU solute binding domain from Streptococcus pneumoniae D39 in complex with L-ergothioneine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Z7E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 Sodium citrate tribasic pH 5.6, Potassium Sodium Tartrate 0.2 M and Ammonium Sulphate 1.8 - 2.0 M
Crystal Properties Matthews coefficient Solvent content 3.2 61.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.999 α = 90 b = 129.017 β = 90 c = 206.906 γ = 90
Symmetry Space Group F 2 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 CMOS RDI CMOS_8M 2021-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.07216 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.78 43.54 99.9 0.081 0.087 0.033 0.998 13.7 7 75117 25.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.82 100 0.983 1.062 0.4 0.824 1.6 7.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4Z7E 1.78 43.54 1.33 75008 3794 99.76 0.16 0.1586 0.159 0.1862 0.187 35.41
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 7.7065 f_angle_d 0.9151 f_chiral_restr 0.0491 f_bond_d 0.007 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4256 Nucleic Acid Atoms Solvent Atoms 539 Heterogen Atoms 67
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing