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Crystal structure of predicted acyltransferase YjdJ with acyl-CoA N-acyltransferase domain from Escherichia coli str. K-12
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M HEPES, 5 mM Cobalt Chloride, 5 mM Magnesium Chloride, 0.5 mM Cadmium Chloride, 0.5 mM Nickel Chloride, 12 % (w/v) PEG3350, 25 Sucrose, 1 mM AcCoA
Crystal Properties Matthews coefficient Solvent content 2.28 46.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.69 α = 90 b = 87.84 β = 90 c = 41.58 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 CCD MARMOSAIC 300 mm CCD 2014-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.92 30.19 98.9 0.038 27.9 7.1 7731
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 1.92 1.97 99.6 0.59 2.9 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.92 30.19 7344 354 98.34 0.21782 0.21551 0.2265 0.26595 0.2843 RANDOM 44.871
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] -1.7 3.13 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.668 r_sphericity_bonded 41.565 r_dihedral_angle_4_deg 21.283 r_dihedral_angle_3_deg 19.694 r_dihedral_angle_1_deg 8.739 r_long_range_B_refined 6.662 r_long_range_B_other 6.539 r_scangle_other 3.552 r_mcangle_other 3.515 r_mcangle_it 3.514
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.668 r_sphericity_bonded 41.565 r_dihedral_angle_4_deg 21.283 r_dihedral_angle_3_deg 19.694 r_dihedral_angle_1_deg 8.739 r_long_range_B_refined 6.662 r_long_range_B_other 6.539 r_scangle_other 3.552 r_mcangle_other 3.515 r_mcangle_it 3.514 r_scbond_it 2.401 r_mcbond_it 2.386 r_mcbond_other 2.361 r_scbond_other 2.327 r_angle_refined_deg 2.223 r_angle_other_deg 1.18 r_chiral_restr 0.147 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 723 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data scaling PHENIX phasing PHENIX model building XDS data reduction