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Crystal structure of Klebsiella pneumoniae FabG2(NADH-dependent) in complex with NADH at 2.5 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JRO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 297 20 % PEG3350
0.2 M Na malonate pH 6.0
12.5 mM NADH added to the protein solution prior to drop mixing
Crystal Properties Matthews coefficient Solvent content 3.24 0.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 161.109 α = 90 b = 255.316 β = 90 c = 262.312 γ = 90
Symmetry Space Group F 2 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 PILATUS3 S 6M Toroidal mirrors 2016-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97625 ESRF ID23-1
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 2.5 48.96 99.3 0.075 0.096 0.044 0.997 10.2 4.3 92045 46.1
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 2.5 2.54 99.5 0.606 0.779 0.369 0.739 2.1 4.4
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 4JRO 2.5 30 87489 4508 99.13 0.1927 0.1917 0.1984 0.2106 0.1905 RANDOM 55.47
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] -0.15 0.74 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.667 r_dihedral_angle_4_deg 18.605 r_dihedral_angle_3_deg 13.841 r_dihedral_angle_1_deg 5.485 r_angle_refined_deg 1.478 r_angle_other_deg 0.938 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.667 r_dihedral_angle_4_deg 18.605 r_dihedral_angle_3_deg 13.841 r_dihedral_angle_1_deg 5.485 r_angle_refined_deg 1.478 r_angle_other_deg 0.938 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14288 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 475
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing