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x-ray structure of the PglF 4,5-dehydratase from campylobacter jejuni, variant M405Y, in complex with UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BJU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 20% PEG-5000, 2% MPD, 10 MM UDP, 100 MM MES
Crystal Properties Matthews coefficient Solvent content 2.52 51.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.508 α = 90 b = 108.273 β = 90 c = 109.657 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 ADSC QUANTUM 210r 2017-06-10 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 1.6 50 94.7 0.066 0.066 58.3 6.6 103648
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 1.6 1.66 88.4 0.126 0.126 10.9 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5BJU 1.6 31 98441 5186 94.62 0.17049 0.16915 0.1834 0.19599 0.2099 RANDOM 21.747
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] -0.79 -1.08 1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.209 r_dihedral_angle_4_deg 19.545 r_dihedral_angle_3_deg 14.408 r_long_range_B_refined 7.254 r_long_range_B_other 7.254 r_dihedral_angle_1_deg 6.05 r_scangle_other 5.646 r_scbond_it 3.783 r_scbond_other 3.78 r_mcangle_other 3.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.209 r_dihedral_angle_4_deg 19.545 r_dihedral_angle_3_deg 14.408 r_long_range_B_refined 7.254 r_long_range_B_other 7.254 r_dihedral_angle_1_deg 6.05 r_scangle_other 5.646 r_scbond_it 3.783 r_scbond_other 3.78 r_mcangle_other 3.072 r_mcangle_it 3.066 r_mcbond_it 2.323 r_mcbond_other 2.308 r_angle_refined_deg 1.871 r_angle_other_deg 0.879 r_chiral_restr 0.117 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 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 5308 Nucleic Acid Atoms Solvent Atoms 726 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing