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Crystal structure of Neisseria gonorrhoeae FabI in complex with NADH and (E)-3-((2R,3S)-3-hydroxy-2-methyl-4-oxo-2,3,4,5-tetrahydro-1H-pyrido[2,3-b][1,4]diazepin-8-yl)-N-methyl-N-((3-methylbenzofuran-2-yl)methyl)acrylamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AHE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 295 100mM Bicine pH9; 2.4M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.41 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.26 α = 90 b = 91.26 β = 90 c = 241.06 γ = 120
Symmetry Space Group P 61 2 2
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 9M 2021-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.34 75.21 96.9 0.058 0.059 0.013 1 26.1 19.8 108279
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.34 1.445 77.7 2.06 2.114 0.472 0.655 1.6 19.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.34 75.21 102908 5371 81.48 0.168 0.1666 0.1673 0.1964 0.1968 RANDOM 20.842
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 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.964 r_dihedral_angle_2_deg 11.478 r_dihedral_angle_1_deg 6.382 r_mcangle_it 2.522 r_angle_refined_deg 2.038 r_mcbond_it 1.896 r_mcbond_other 1.895 r_angle_other_deg 0.657 r_chiral_restr 0.098 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.964 r_dihedral_angle_2_deg 11.478 r_dihedral_angle_1_deg 6.382 r_mcangle_it 2.522 r_angle_refined_deg 2.038 r_mcbond_it 1.896 r_mcbond_other 1.895 r_angle_other_deg 0.657 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3836 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement PHASER phasing PDB_EXTRACT data extraction autoPROC data reduction autoPROC data scaling