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2.25 Angstrom Resolution Crystal Structure of Fatty-Acid-CoA Ligase (FadD32) from Mycobacterium smegmatis in complex with Inhibitor 5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HM3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 Protein: 15.2mg/ml, 0.01M Tris-HCL buffer pH(8.3), 0.5mM TCEP;
Screen: PACT (G6), 0.2M Sodium formate, 0.1M Bis-Tris propane pH 7.5, 20%(w/v) PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.46 50.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.294 α = 90 b = 153.561 β = 90 c = 201.253 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 CCD MARMOSAIC 300 mm CCD C(111) 2015-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.25 30 100 0.081 0.081 0.842 24.1 7.5 133115 -3 42.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.29 100 0.699 3.1 7.5
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 5HM3 2.25 29.86 126351 6648 99.92 0.17494 0.17263 0.1779 0.21907 0.2196 RANDOM 48.823
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] -1.08 2.47 -1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.597 r_dihedral_angle_4_deg 12.254 r_dihedral_angle_3_deg 10.76 r_long_range_B_refined 6.517 r_long_range_B_other 6.358 r_scangle_other 3.281 r_mcangle_it 3.121 r_mcangle_other 3.121 r_dihedral_angle_1_deg 2.44 r_scbond_it 2.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.597 r_dihedral_angle_4_deg 12.254 r_dihedral_angle_3_deg 10.76 r_long_range_B_refined 6.517 r_long_range_B_other 6.358 r_scangle_other 3.281 r_mcangle_it 3.121 r_mcangle_other 3.121 r_dihedral_angle_1_deg 2.44 r_scbond_it 2.075 r_scbond_other 2.075 r_mcbond_it 1.834 r_mcbond_other 1.834 r_angle_refined_deg 1.554 r_angle_other_deg 0.926 r_chiral_restr 0.094 r_gen_planes_refined 0.022 r_gen_planes_other 0.018 r_bond_refined_d 0.011 r_bond_other_d 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 18704 Nucleic Acid Atoms Solvent Atoms 1125 Heterogen Atoms 200
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing