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Specific recognition of N-acetylated substrates and domain flexibility in WbgU: a UDP-GalNAc 4-epimerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LU1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 6.5 298.15 25% PEG 3350, 0.2 M Ammonium Sulfate, 200 mM Bis Tris Propane pH 6.5
, microbatch under oil, temperature 298.15K
Crystal Properties Matthews coefficient Solvent content 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.282 α = 90 b = 78.282 β = 90 c = 231.797 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 103 CCD ADSC QUANTUM 315r 2011-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.98 APS 19-ID
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 2.1 50 100 92338 92338 2 2
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 2.1 2.14 100
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 3LU1 2.1 50 2 87697 4641 98.84 0.21793 0.21514 0.2196 0.26955 0.2753 RANDOM 31.694
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] -0.98 -0.49 -0.98 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.356 r_dihedral_angle_3_deg 17.159 r_dihedral_angle_4_deg 16.678 r_dihedral_angle_1_deg 6.957 r_scangle_it 3.572 r_scbond_it 2.552 r_angle_refined_deg 1.872 r_mcangle_it 1.451 r_mcbond_it 0.909 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.356 r_dihedral_angle_3_deg 17.159 r_dihedral_angle_4_deg 16.678 r_dihedral_angle_1_deg 6.957 r_scangle_it 3.572 r_scbond_it 2.552 r_angle_refined_deg 1.872 r_mcangle_it 1.451 r_mcbond_it 0.909 r_chiral_restr 0.122 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 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 10704 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 342
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling