☰ Navigation Tabs
Crystal structure WlaRD, a sugar 3N-formyl transferase in the presence of dTDP and 10-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 TDP, 5 mM N-5-Formyl-THF, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.14 60.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.337 α = 90 b = 65.858 β = 109.88 c = 134.6 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 Bruker Platinum 135 mirrors 2013-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 1.64 50 96.2 0.058 0.058 14.6 4 93525 93525
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 1.64 1.74 86.6 0.364 0.364 2.2 2.2 13710
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 1.64 48.21 93525 88820 4704 96.12 0.191 0.19095 0.18911 0.198 0.22564 0.232 RANDOM 18.836
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] 0.15 -0.29 1.22 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.809 r_dihedral_angle_4_deg 14.107 r_dihedral_angle_3_deg 13.723 r_dihedral_angle_1_deg 7.817 r_angle_refined_deg 2.078 r_angle_other_deg 0.908 r_chiral_restr 0.131 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.809 r_dihedral_angle_4_deg 14.107 r_dihedral_angle_3_deg 13.723 r_dihedral_angle_1_deg 7.817 r_angle_refined_deg 2.078 r_angle_other_deg 0.908 r_chiral_restr 0.131 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 4489 Nucleic Acid Atoms Solvent Atoms 795 Heterogen Atoms 144
Software Software Software Name Purpose APEX data collection PHASER phasing REFMAC refinement APEX data reduction