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1.84 Angstrom resolution crystal structure of 3-oxoacyl-(acyl carrier protein) synthase I (fabB) from Yersinia pestis CO92
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SAD model of the data set collected on 21-ID-G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 Crystallization condition: 20%PEG 8K, 0.05M K dihydrogen Phosphate. Paratone-N was used as cryoprotectant, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.11 41.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.649 α = 90 b = 114.613 β = 90 c = 59.157 γ = 90
Symmetry Space Group P 21 21 2
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 Be Lenses/Diamond Laue Mono 2010-07-31 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MAR CCD Mirror 2010-08-13 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 2 SYNCHROTRON APS BEAMLINE 21-ID-D 0.77483 APS 21-ID-D
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 1.84 30 99.6 0.127 13.13 5.7 64383 64383 -3
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) 1.84 1.88 97.3 0.592 2.55 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD model of the data set collected on 21-ID-G 1.84 29.58 61048 61048 3270 98.95 0.15727 0.15536 0.1593 0.19294 0.1956 RANDOM 19.043
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] -0.98 2.25 -1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.282 r_dihedral_angle_4_deg 10.665 r_dihedral_angle_3_deg 9.191 r_scangle_it 3.474 r_scbond_it 2.358 r_dihedral_angle_1_deg 2.255 r_angle_refined_deg 1.659 r_mcangle_it 1.152 r_angle_other_deg 0.873 r_mcbond_it 0.616
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.282 r_dihedral_angle_4_deg 10.665 r_dihedral_angle_3_deg 9.191 r_scangle_it 3.474 r_scbond_it 2.358 r_dihedral_angle_1_deg 2.255 r_angle_refined_deg 1.659 r_mcangle_it 1.152 r_angle_other_deg 0.873 r_mcbond_it 0.616 r_mcbond_other 0.165 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5924 Nucleic Acid Atoms Solvent Atoms 651 Heterogen Atoms 125
Software Software Software Name Purpose Blu-Ice data collection PHENIX model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing