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Crystal structure of PflD bound to 1,5-anhydromannitol-6-phosphate in Streptococcus dysgalactiae subsp. equisimilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other Molecular replacement was performed by PHENIX using predicted structural model of PflD by Phyre2 server.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 1.2 M sodium citrate, 0.1 M sodium HEPES, pH 8.0, 10 mM 1,5-anhydromannitol-6-phosphate
Crystal Properties Matthews coefficient Solvent content 3.32 62.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.912 α = 90 b = 183.912 β = 90 c = 60.025 γ = 120
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 EIGER X 16M 2022-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.9792 SSRF BL10U2
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 2.34 159.27 100 0.199 0.317 0.105 0.983 12.3 9.6 49308
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.34 2.4 1.792 0.82 0.446 8
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 2.34 60.199 48714 1960 98.8 0.1583 0.1569 0.158 0.1929 0.1918
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 7.91 f_angle_d 0.843 f_chiral_restr 0.051 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6103 Nucleic Acid Atoms Solvent Atoms 564 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHENIX phasing