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Crystal Structure of VldE, the pseudo-glycosyltransferase, in complex with GDP
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, 3 mM GDP, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.21 44.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.029 α = 90 b = 121.037 β = 90 c = 47.824 γ = 90
Symmetry Space Group P 21 21 2
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 0.9792 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 2.55 44.48 98 16553 16222 2.8 2.8
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 2.55 2.69 86.8
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 2.55 44.48 2.8 15385 15385 814 100 0.24296 0.24064 0.242 0.28573 0.2859 RANDOM 42.266
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] 1.94 -0.49 -1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.889 r_dihedral_angle_4_deg 20.092 r_dihedral_angle_3_deg 18.72 r_dihedral_angle_1_deg 5.523 r_scangle_it 3.001 r_scbond_it 1.881 r_angle_refined_deg 1.556 r_mcangle_it 1.167 r_mcbond_it 0.646 r_chiral_restr 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.889 r_dihedral_angle_4_deg 20.092 r_dihedral_angle_3_deg 18.72 r_dihedral_angle_1_deg 5.523 r_scangle_it 3.001 r_scbond_it 1.881 r_angle_refined_deg 1.556 r_mcangle_it 1.167 r_mcbond_it 0.646 r_chiral_restr 0.105 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3704 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 28
Software Software Software Name Purpose ADSC data collection PHENIX model building REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing