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Crystal structure of the GDP-D-glycero-4-keto-D-lyxo-heptose-3-epimerase from campylobacter jejuni, serotype HS:23/36
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 8 293 Protein incubated with 5 mM GDP; precipitant: 18-20% PEG3350, 200 mM potassium chloride, 100 mM HEPES, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.08 40.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.84 α = 83.25 b = 44.766 β = 79.35 c = 57.428 γ = 65.08
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 2020-12-18 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 1.55 50 93.9 0.049 15.5 3.5 48120
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 1.55 1.65 85 0.258 3.6 1.9
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 1.55 35.75 45672 2448 93.85 0.1667 0.1649 0.1748 0.2004 0.212 RANDOM 15.814
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 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.053 r_dihedral_angle_3_deg 13.174 r_dihedral_angle_4_deg 12.741 r_dihedral_angle_1_deg 8.136 r_angle_refined_deg 1.76 r_angle_other_deg 1.502 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.053 r_dihedral_angle_3_deg 13.174 r_dihedral_angle_4_deg 12.741 r_dihedral_angle_1_deg 8.136 r_angle_refined_deg 1.76 r_angle_other_deg 1.502 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2943 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction SADABS data scaling PHASER phasing