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Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase III from Burkholderia xenovorans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HN9 PDB entry 1HN9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 Internal tracking number 228627G11. Crystallant (Wizard III/IV G11): 20% PEG 6000, 0.1 M Hepes pH 7.0, 200 mM NaCl. Protein: BuxeA.00171.c.A1 PW33645 at 35 mg/ml in a buffer consisting of 25 mM HEPES pH 7.0, 300-500 mM NaCl, 2 mM DTT, 0.025% sodium azide, 5% glycerol. Cryoprotection was achieved by supplementing the reservoir solution with 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.99 α = 113.72 b = 67.03 β = 89.98 c = 89.2 γ = 100.25
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 ADSC QUANTUM 315 2011-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
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 2.35 50 97.8 0.087 11.9 3.3 49242 -3 36.372
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 2.35 2.41 97.5 0.502 2.5 3.3
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 MR, MR THROUGHOUT PDB entry 1HN9 2.35 50 49242 2488 97.98 0.229 0.227 0.2272 0.275 0.2755 RANDOM 30.633
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 -0.43 -1.09 -0.37 1.88 1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.696 r_dihedral_angle_4_deg 19.836 r_dihedral_angle_3_deg 15.564 r_dihedral_angle_1_deg 7.069 r_angle_refined_deg 1.294 r_angle_other_deg 1.167 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.696 r_dihedral_angle_4_deg 19.836 r_dihedral_angle_3_deg 15.564 r_dihedral_angle_1_deg 7.069 r_angle_refined_deg 1.294 r_angle_other_deg 1.167 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9403 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 4
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction