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Crystal structure WlaRD, a sugar 3N-formyl transferase in the presence of dTdp and 5-N-Formyl-THF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LXT pdb entry 4LXT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 11-15% PEG 8000, 200 mM NaCl, 5 mM dTDP, 5 mM N5-formyl-THF, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.1 60.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.861 α = 90 b = 63.259 β = 110.04 c = 136.212 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 1.4 30 97 0.046 0.046 56.7 4.8 148911 148911
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 1.4 1.45 91.7 0.077 0.077 18.8 2.9 14019
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 (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 4LXT 1.4 30 148911 141466 7445 96.89 0.15931 0.15827 0.1572 0.17848 0.177 RANDOM 16.596
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] -0.1 -0.07 0.7 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.753 r_dihedral_angle_4_deg 16.421 r_dihedral_angle_3_deg 12.297 r_dihedral_angle_1_deg 7.337 r_scangle_it 5.384 r_scbond_it 3.507 r_mcangle_it 2.337 r_angle_refined_deg 1.874 r_mcbond_it 1.433 r_chiral_restr 0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.753 r_dihedral_angle_4_deg 16.421 r_dihedral_angle_3_deg 12.297 r_dihedral_angle_1_deg 7.337 r_scangle_it 5.384 r_scbond_it 3.507 r_mcangle_it 2.337 r_angle_refined_deg 1.874 r_mcbond_it 1.433 r_chiral_restr 0.131 r_gen_planes_refined 0.013 r_bond_refined_d 0.012 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 1016 Heterogen Atoms 221
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling