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High Resolution Crystal Structure of Enterococcus faecium Nicotinate Nucleotide Adenylyltransferase Complexed with Adenine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Homology structure generated by AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 293 15 mg/mL EfNNAT in 50mM HEPES, 2mM DTT, 150mM NaCl, 0.02% NaN3 at pH 7.2 with the crystallization buffer consisting of 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS (pH 5.5), 25% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.15 42.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.511 α = 90 b = 65.644 β = 90 c = 108.373 γ = 90
Symmetry Space Group I 21 21 21
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 EIGER2 XE 16M 2022-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.82 45.269 98.7 0.116 0.121 0.033 0.998 10.4 13.5 19984
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.85 97.7 0.418 0.4 14
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 THROUGHOUT Homology structure generated by AlphaFold 1.82 45.269 1.33 19327 935 94.83 0.2071 0.2057 0.2114 0.2332 0.233 56.9304
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1468 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction DIALS data reduction DIALS data scaling MrBUMP phasing