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Crystal Structure of VldE, the pseudo-glycosyltransferase which catalyzes non-glycosidic C-N coupling in Validamycin A biosynthesis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 100 mM Tris-HCl, pH 8.0, 20-35% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.31 46.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.237 α = 90 b = 48.562 β = 91.88 c = 123.049 γ = 90
Symmetry Space Group P 1 2 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 CCD ADSC QUANTUM 315 2011-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9479 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.98 122.983 98.1 70660 69317 2.7 2.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.08 91.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 1.98 49.103 2.7 67391 66548 3559 98.75 0.18933 0.18754 0.1994 0.22191 0.2315 RANDOM 41.854
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] -0.49 -0.44 0.31 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.673 r_dihedral_angle_4_deg 16.296 r_dihedral_angle_3_deg 15.149 r_dihedral_angle_1_deg 5.475 r_scangle_it 5.15 r_scbond_it 3.47 r_mcangle_it 2.124 r_angle_refined_deg 1.673 r_mcbond_it 1.372 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.673 r_dihedral_angle_4_deg 16.296 r_dihedral_angle_3_deg 15.149 r_dihedral_angle_1_deg 5.475 r_scangle_it 5.15 r_scbond_it 3.47 r_mcangle_it 2.124 r_angle_refined_deg 1.673 r_mcbond_it 1.372 r_chiral_restr 0.126 r_bond_refined_d 0.022 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7474 Nucleic Acid Atoms Solvent Atoms 489 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHENIX model building REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing