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Crystal Structure of S-adenosyl-l-homocysteine Hydrolase from Naegleria fowleri with bound NAD and Adenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OND
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 NafoA.00032.a.B1.PW37932 at 19.8 mg/ml incubated with 3 mM each SAH and NAD, then mixed 1:1 with an equal volume JCSG+(c4): 10% (w/v) PEG-6000, 0.1 M HEPES free acid/NaOH, pH = 7.0, cryoprotected with 20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.66 53.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.83 α = 90 b = 134.33 β = 90 c = 239.79 γ = 90
Symmetry Space Group P 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 CCD MARMOSAIC 300 mm CCD Beryllium Lenses 2017-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 48.408 99.9 0.093 0.101 0.998 16.01 6.244 152740 -3 19.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 100 0.498 0.543 0.903 3.89 6.286
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 3OND 2 48.408 1.34 152736 1977 99.92 0.1388 0.1383 0.1391 0.1797 0.18 22.5332
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 14.307 f_angle_d 0.868 f_chiral_restr 0.055 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14187 Nucleic Acid Atoms Solvent Atoms 1716 Heterogen Atoms 484
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction MoRDa phasing