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The X-ray crystal structure of the Streptococcus pneumoniae Fatty Acid Kinase (Fak) B2 protein loaded with cis-oleic acid to 1.9 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other MODBASE sequence based generated 3D model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 0.1M HEPES pH 7.4, 10% v/v isopropanol, 20% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.45 49.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.72 α = 90 b = 103.851 β = 90 c = 108.174 γ = 90
Symmetry Space Group P 21 21 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 EIGER X 16M 2018-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
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 1.9 74.92 98.3 0.109 0.129 0.067 0.993 9.4 3.7 52631 17.034
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 1.9 1.94 99.6 0.683 0.896 0.51 0.479 1.9 3.7
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 MODBASE sequence based generated 3D model 1.9 54.15 49927 2659 97.85 0.17333 0.17053 0.1817 0.22655 0.2374 RANDOM 24.118
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] 0.12 1.86 -1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.402 r_dihedral_angle_3_deg 14.266 r_dihedral_angle_4_deg 12.551 r_dihedral_angle_1_deg 6.335 r_long_range_B_refined 6.335 r_long_range_B_other 6.334 r_scangle_other 4.718 r_scbond_it 2.963 r_scbond_other 2.962 r_mcangle_it 2.545
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.402 r_dihedral_angle_3_deg 14.266 r_dihedral_angle_4_deg 12.551 r_dihedral_angle_1_deg 6.335 r_long_range_B_refined 6.335 r_long_range_B_other 6.334 r_scangle_other 4.718 r_scbond_it 2.963 r_scbond_other 2.962 r_mcangle_it 2.545 r_mcangle_other 2.545 r_mcbond_it 1.679 r_mcbond_other 1.679 r_angle_refined_deg 1.361 r_angle_other_deg 0.923 r_chiral_restr 0.065 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4282 Nucleic Acid Atoms Solvent Atoms 551 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing