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Crystal structure of the N-terminal domain of fatty acid kinase A (FakA) from Staphylococcus aureus (Mg and ADP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8VIP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 291 Proplex C3: 20% (w/v) PEG 4000, 100 mM sodium acetate pH 5.0, 200 mM ammonium acetate, Cryo: 80% well solution and 20% (v/v) PEG 200, 2.5 mM MgCl2 and 2.5 mM ADP added to the protein prior to crystallization.
Crystal Properties Matthews coefficient Solvent content 2 38.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.936 α = 90 b = 57.094 β = 90 c = 81.029 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 PILATUS 6M 2019-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-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 1.25 46.67 100 0.053 0.058 0.023 0.999 14.2 6.3 55921
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 1.25 1.27 100 1.152 1.263 0.511 0.754 6
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 1.25 34.32 1.04 55824 2753 99.91 0.139 0.1379 0.1517 0.1607 0.1755
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 18.315 f_angle_d 0.98 f_chiral_restr 0.066 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1547 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing