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Crystal structure WlaRD, a sugar 3N-formyl transferase in the presence of dTdp-Qui3N 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 7 295 11-15% PEG 8000, 200 mM NaCl, 5 mM N-5formyl-THF, 5 mM TDP-Qui3N, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.11 60.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.775 α = 90 b = 65.148 β = 110.51 c = 134.718 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 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 92.9 0.045 0.045 48.3 3.8 143095
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 84.9 0.08 0.08 15.5 2.4
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 4LXQ 1.4 30 143095 135924 7171 92.9 0.179 0.177 0.1772 0.206 0.205 RANDOM 18.45
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] 0.14 -0.17 0.61 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.475 r_dihedral_angle_3_deg 12.993 r_dihedral_angle_4_deg 11.719 r_dihedral_angle_1_deg 7.545 r_scangle_it 5.598 r_scbond_it 3.742 r_mcangle_it 2.513 r_angle_refined_deg 2.071 r_mcbond_it 1.672 r_chiral_restr 0.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.475 r_dihedral_angle_3_deg 12.993 r_dihedral_angle_4_deg 11.719 r_dihedral_angle_1_deg 7.545 r_scangle_it 5.598 r_scbond_it 3.742 r_mcangle_it 2.513 r_angle_refined_deg 2.071 r_mcbond_it 1.672 r_chiral_restr 0.142 r_bond_refined_d 0.015 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_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 946 Heterogen Atoms 216
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling