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Crystal structure of CJ1428, a GDP-D-GLYCERO-L-GLUCO-HEPTOSE SYNTHASE from campylobacter jejuni in the presence of NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FXS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 16-20% PEG-5000, 150 mM MgCL2, 100 mM MOPS
Crystal Properties Matthews coefficient Solvent content 2.72 54.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.365 α = 90 b = 131.326 β = 105.76 c = 58.855 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 CCD ADSC QUANTUM 210r 2019-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9878 APS 19-BM
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 96.9 0.069 35.5 3.9 129208
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 1.53 92.9 0.253 3.8 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 1fxs 1.5 30.95 122651 6557 96.75 0.1637 0.1627 0.1654 0.183 0.1862 RANDOM 22.485
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 -0.6 1.45 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.258 r_dihedral_angle_4_deg 16.609 r_dihedral_angle_3_deg 15.162 r_dihedral_angle_1_deg 6.69 r_angle_refined_deg 1.641 r_angle_other_deg 1.473 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.258 r_dihedral_angle_4_deg 16.609 r_dihedral_angle_3_deg 15.162 r_dihedral_angle_1_deg 6.69 r_angle_refined_deg 1.641 r_angle_other_deg 1.473 r_chiral_restr 0.084 r_bond_refined_d 0.01 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 5429 Nucleic Acid Atoms Solvent Atoms 656 Heterogen Atoms 103
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing