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High-resolution crystal structure of Vibrio cholerae NFeoB bound to GDP-AlF3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8VWL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 25 % (w/v) PEG3350, 0.1 M HEPES, pH 7.5, 0.5 mM GDP, 5 mM magnesium chloride, 5 mM sodium fluoride, 0.5 mM aluminum trichloride
Crystal Properties Matthews coefficient Solvent content 2.23 44.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.238 α = 94.439 b = 59.077 β = 92.373 c = 89.634 γ = 113.535
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 DECTRIS EIGER X 16M 2025-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97934 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 34.52 91.9 0.986 4 3.4 62735 22.27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.04 97.1 0.329
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 32.72 1.97 62614 3147 91.72 0.1903 0.1875 0.1895 0.2419 0.24 29
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.3021 f_angle_d 0.9612 f_chiral_restr 0.0556 f_plane_restr 0.0074 f_bond_d 0.0073
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8130 Nucleic Acid Atoms Solvent Atoms 618 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement PHASER phasing autoPROC data reduction autoPROC data scaling