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Crystal structure WlaRD, a sugar 3N-formyl transferase in the presence of dTDP-Fuc3NFo and 5-N-Formyl-THF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LXQ PDB entry 4LXQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 11-15% PEG 8000, 200 mM NaCl, 5 mM N-5-formyl-THF, 5 mM TDP-Fuc3NFo, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.11 60.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.992 α = 90 b = 64.825 β = 110.6 c = 134.798 γ = 90
Symmetry Space Group C 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 210r 2012-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9794 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 1.45 30 94.5 0.071 0.071 56.4 4.6 130605 130605
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.5 85.5 0.12 0.12 11.5 2.8 11745
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 4LXQ 1.45 30 130605 124054 6551 94.44 0.183 0.1827 0.18115 0.1811 0.2118 0.2113 RANDOM 19.148
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] 0.43 -0.08 0.51 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.029 r_dihedral_angle_4_deg 14.812 r_dihedral_angle_3_deg 13.971 r_dihedral_angle_1_deg 7.802 r_scangle_it 6.096 r_scbond_it 4.059 r_mcangle_it 2.814 r_mcbond_it 1.87 r_angle_refined_deg 1.71 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.029 r_dihedral_angle_4_deg 14.812 r_dihedral_angle_3_deg 13.971 r_dihedral_angle_1_deg 7.802 r_scangle_it 6.096 r_scbond_it 4.059 r_mcangle_it 2.814 r_mcbond_it 1.87 r_angle_refined_deg 1.71 r_chiral_restr 0.127 r_bond_refined_d 0.012 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4511 Nucleic Acid Atoms Solvent Atoms 764 Heterogen Atoms 211
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling