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X-ray structure of the GDP-6-deoxy-4-keto-D-lyxo-heptose-4-reductase from Campylobacter jejuni HS:15
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7M13 PDB entry 7M13
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Protein pre-incubated with 5.0 mM GDP, 5.0 mM NADPH. Precipitant: 18-22% PEG3350, 2% isopropanol, 100 mM HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.13 42.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.761 α = 87.96 b = 56.625 β = 81.96 c = 67.38 γ = 70.12
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL Bruker PHOTON II 2021-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.45 50 96.2 0.049 18.4 6.8 121498
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.55 87.9 0.338 3.2 3.2
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 PDB entry 7M13 1.45 33.38 115400 6098 96.16 0.1899 0.1884 0.1958 0.2187 0.2234 RANDOM 16.068
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.276 r_dihedral_angle_3_deg 14.435 r_dihedral_angle_4_deg 8.349 r_dihedral_angle_1_deg 6.675 r_angle_refined_deg 1.743 r_angle_other_deg 1.491 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.276 r_dihedral_angle_3_deg 14.435 r_dihedral_angle_4_deg 8.349 r_dihedral_angle_1_deg 6.675 r_angle_refined_deg 1.743 r_angle_other_deg 1.491 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5739 Nucleic Acid Atoms Solvent Atoms 700 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction SADABS data scaling PHASER phasing