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x-ray structure of cj1430 in the presence of GDP, a GDP-D-glycero-4-keto-D-lyxo-heptose-3,5-epimerase from campylobacter jejuni
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RYK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 22-27% PEG-5000, 100 mM MOPS, 10 mM GDP
Crystal Properties Matthews coefficient Solvent content 2.4 48.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.286 α = 90 b = 83.709 β = 94.74 c = 110.044 γ = 90
Symmetry Space Group C 1 2 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 2020-08-29 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 2.1 50 97.3 0.088 9.7 5.2 69127
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 2.1 2.2 93 0.39 2.4
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 3ryk 2.1 27.83 65719 3408 97.31 0.2049 0.2018 0.2088 0.2638 0.2656 RANDOM 26.749
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] -1.49 -0.12 1.63 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.656 r_dihedral_angle_4_deg 17.34 r_dihedral_angle_3_deg 17.069 r_dihedral_angle_1_deg 8.562 r_angle_refined_deg 1.595 r_angle_other_deg 1.222 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.656 r_dihedral_angle_4_deg 17.34 r_dihedral_angle_3_deg 17.069 r_dihedral_angle_1_deg 8.562 r_angle_refined_deg 1.595 r_angle_other_deg 1.222 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8738 Nucleic Acid Atoms Solvent Atoms 645 Heterogen Atoms 177
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction PROTEUM PLUS data reduction SADABS data scaling PHASER phasing