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Crystal structure of the GDP-D-glycero-4-keto-d-lyxo-heptose-3,5-epimerase from Campylobacter jejuni, serotype HS:15
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 7 293 Enzyme pre-incubated with 5 mM GDP; precipitant: 26-28% PEG8000, 100 mM MES
Crystal Properties Matthews coefficient Solvent content 2.26 45.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.549 α = 90 b = 154.525 β = 91.28 c = 120.506 γ = 90
Symmetry Space Group P 1 21 1
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 2021-07-21 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) Rpim I (All) 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 1.9 50 99.3 0.081 9.3 4.5 118325
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 1.9 1.95 96.9 0.389 2.5 2.8
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 PDB entry 7M14 1.9 36.81 112415 5910 99.26 0.1913 0.1889 0.1957 0.2357 0.2413 RANDOM 14.664
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 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.778 r_dihedral_angle_3_deg 15.057 r_dihedral_angle_4_deg 14.394 r_dihedral_angle_1_deg 8.532 r_angle_refined_deg 1.613 r_angle_other_deg 1.273 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.778 r_dihedral_angle_3_deg 15.057 r_dihedral_angle_4_deg 14.394 r_dihedral_angle_1_deg 8.532 r_angle_refined_deg 1.613 r_angle_other_deg 1.273 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11618 Nucleic Acid Atoms Solvent Atoms 1045 Heterogen Atoms 231
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction SADABS data scaling PHASER phasing