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X-ray structure of the PglF dehydratase from Campylobacter jejuni in complex with UDP and NAD(H)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 22% PEG-5000, 2% MPD, 10 mM UDP, 100 mM MES
Crystal Properties Matthews coefficient Solvent content 2.52 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.135 α = 90 b = 107.882 β = 90 c = 110.208 γ = 90
Symmetry Space Group P 21 21 21
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 2016-09-06 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 2 50 97.3 0.092 0.092 13.2 3.7 54971
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 2 2.1 93.4 0.253 0.253 4.6 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 2 30 52185 2728 97.35 0.19519 0.19303 0.2045 0.23673 0.2476 RANDOM 17.679
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] -0.73 -0.27 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.642 r_dihedral_angle_4_deg 21.519 r_dihedral_angle_3_deg 15.703 r_dihedral_angle_1_deg 6.983 r_long_range_B_refined 6.065 r_long_range_B_other 6.064 r_scangle_other 4.554 r_scbond_it 2.858 r_scbond_other 2.857 r_mcangle_it 2.627
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.642 r_dihedral_angle_4_deg 21.519 r_dihedral_angle_3_deg 15.703 r_dihedral_angle_1_deg 6.983 r_long_range_B_refined 6.065 r_long_range_B_other 6.064 r_scangle_other 4.554 r_scbond_it 2.858 r_scbond_other 2.857 r_mcangle_it 2.627 r_mcangle_other 2.627 r_mcbond_it 1.771 r_mcbond_other 1.75 r_angle_refined_deg 1.701 r_angle_other_deg 0.807 r_chiral_restr 0.094 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5283 Nucleic Acid Atoms Solvent Atoms 489 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing