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Crystal structure of NAD synthetase (NadE) from Enterococcus faecalis in complex with NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HUJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 0.1 M Bis-tris pH 5.5, 0.2 M magnesium chloride, 25% (w/v) PEG3350, 10 mM NAD+
Crystal Properties Matthews coefficient Solvent content 2.62 53.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.445 α = 90 b = 85.165 β = 94.54 c = 175.811 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2017-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.6 25 99.2 0.117 0.076 7.8 3.2 77971
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 2.6 2.64 94.9 0.723 0.495 0.651 0.83
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5huj 2.583 24.776 1.35 77904 2018 98.43 0.1888 0.1875 0.1891 0.239 0.2396 RANDOM
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 21.236 f_angle_d 0.54 f_chiral_restr 0.039 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16539 Nucleic Acid Atoms Solvent Atoms 927 Heterogen Atoms 335
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing PHENIX model building Coot model building