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Crystal structure of Klebsiella pneumoniae FabG(NADPH-dependent) NADP-complex at 1.75 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q7B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 297 9.5 mg/ml protein solution mixed with
NADP+ at 11.5 mM concentration
Well solution:
0.1 M phosphate-citrate 4.2 pH
40 %v/v PEG 300
Crystal Properties Matthews coefficient Solvent content 2.39 48.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.723 α = 90 b = 118.842 β = 90 c = 119.759 γ = 90
Symmetry Space Group C 2 2 21
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 2017-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.96862 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 59.88 96.8 0.034 0.026 0.998 15 3.8 47966 27.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 99.3 0.38 0.297 0.861 2 3.8
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 1Q7B 1.75 59.88 45483 2449 96.4 0.1596 0.1579 0.1686 0.1938 0.1997 RANDOM 38.978
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] 2.4 -1.82 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.331 r_dihedral_angle_4_deg 15.683 r_dihedral_angle_3_deg 13.766 r_dihedral_angle_1_deg 5.703 r_angle_other_deg 3.738 r_angle_refined_deg 1.853 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_other 0.013 r_gen_planes_refined 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.331 r_dihedral_angle_4_deg 15.683 r_dihedral_angle_3_deg 13.766 r_dihedral_angle_1_deg 5.703 r_angle_other_deg 3.738 r_angle_refined_deg 1.853 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_other 0.013 r_gen_planes_refined 0.008 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3568 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing