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Crystal structure of the GDP-D-glycero-4-keto-d-lyxo-heptose-3-epimerase from Campylobacter jejuni, serotype HS:3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7M14 PDB entry 7M14
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 10-12% PEG8000, 0.75 M tetramethylammonium chloride, 100 mM homopiperazine-1,4-bis(2-ethanesulfonic acid), pH 5.0, protein pre-incubated with 5 mM GDP
Crystal Properties Matthews coefficient Solvent content 2.37 48.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.534 α = 90 b = 67.932 β = 90 c = 96.125 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 PIXEL Bruker PHOTON II 2021-07-20 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 1.5 50 97.5 0.094 11.4 5.7 63904
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 1.5 1.6 89.6 0.369 2.8 2.7
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 7M14 1.5 33.1 60748 3156 97.47 0.1932 0.1919 0.1967 0.2188 0.223 RANDOM 9.26
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.565 r_dihedral_angle_4_deg 15.207 r_dihedral_angle_3_deg 13.926 r_dihedral_angle_1_deg 8.363 r_angle_refined_deg 1.596 r_angle_other_deg 1.374 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.565 r_dihedral_angle_4_deg 15.207 r_dihedral_angle_3_deg 13.926 r_dihedral_angle_1_deg 8.363 r_angle_refined_deg 1.596 r_angle_other_deg 1.374 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2882 Nucleic Acid Atoms Solvent Atoms 496 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction SADABS data scaling PHASER phasing