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The structure of Beta-ketoacyl synthase from Brucella melitensis bound to the fragment 7-hydroxycoumarin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LRF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 BrabA.00113.a at 22.94 mg/ml. 0.2M Sodium malonate, 0.1M Bis tris propane pH8.5, 20% PEG3350. BrabA.00113.a.A1 PW25441, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.39 48.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.56 α = 90 b = 83.25 β = 121.2 c = 73.81 γ = 90
Symmetry Space Group C 1 2 1
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 2010-11-09 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 1.25 39.275 97.8 0.061 15.27 109758 -3 13.707
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 1.25 1.28 93 0.35 3.63
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 Direct phasing from previous structure THROUGHOUT 3LRF 1.25 39.275 109671 5497 97.97 0.1226 0.122 0.1292 0.1341 0.1419 RANDOM 10.2718
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] 0.02 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.838 r_dihedral_angle_4_deg 16.157 r_sphericity_free 14.457 r_dihedral_angle_3_deg 11.343 r_rigid_bond_restr 9.49 r_dihedral_angle_1_deg 6.175 r_sphericity_bonded 3.872 r_angle_other_deg 1.713 r_angle_refined_deg 1.326 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.838 r_dihedral_angle_4_deg 16.157 r_sphericity_free 14.457 r_dihedral_angle_3_deg 11.343 r_rigid_bond_restr 9.49 r_dihedral_angle_1_deg 6.175 r_sphericity_bonded 3.872 r_angle_other_deg 1.713 r_angle_refined_deg 1.326 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3016 Nucleic Acid Atoms Solvent Atoms 520 Heterogen Atoms 19
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing