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Crystal structure of 3-oxoacyl-(acyl carrier protein) synthase II from Brucella melitensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E60 PDB ENTRY 3E60
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 Hampton CSHT condition B5: 0.2 M lithium sulfate, 0.1 M Tris pH 8.5, 30% w/v PEG 4000, 25% ethylene glycol as cryo-protectant, 51.0 mg/mL protein, crystal tracking ID 205856b5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.28 45.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.02 α = 90 b = 62.32 β = 109.18 c = 177.72 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 ADSC QUANTUM 315r 2009-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.979464 SSRL BL7-1
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 1.75 50 96.7 0.05 21.32 4.5 536301 119229 -3 22.489
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 1.75 1.8 90.5 0.285 4.4 3.9 8234
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 PDB ENTRY 3E60 1.75 50 119225 5996 96.8 0.15 0.148 0.1488 0.181 0.1814 RANDOM 10.905
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] -0.81 0.09 1.44 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.249 r_dihedral_angle_4_deg 15.686 r_dihedral_angle_3_deg 12.204 r_dihedral_angle_1_deg 5.547 r_scangle_it 3.319 r_scbond_it 2.027 r_angle_refined_deg 1.343 r_mcangle_it 1.084 r_mcbond_it 0.636 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.249 r_dihedral_angle_4_deg 15.686 r_dihedral_angle_3_deg 12.204 r_dihedral_angle_1_deg 5.547 r_scangle_it 3.319 r_scbond_it 2.027 r_angle_refined_deg 1.343 r_mcangle_it 1.084 r_mcbond_it 0.636 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9221 Nucleic Acid Atoms Solvent Atoms 1268 Heterogen Atoms 27
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction