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Crystal structure of 3-oxoacyl-(acyl carrier protein) synthase II from Bartonella henselae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W0I 1W0I WITH INSERTIONS REMOVED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 289 ProPlex condition B12, 15% PEG 4000, 0.1 M MgCl2, 0.1 M Hepes-NaOH pH 7.0, 0.4/0.4uL drops, 6.5 mg/mL protein, Crystal ID 200083b12, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.91 57.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.339 α = 90 b = 91.339 β = 90 c = 251.177 γ = 90
Symmetry Space Group P 43 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 SI(111) DOUBLE CRYSTAL MONOCHROMETER 2008-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D APS 23-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 1.95 50 99.9 0.123 13.4 7.3 78307
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) 1.95 2.06 100 0.578 3.8 7.4
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 1W0I WITH INSERTIONS REMOVED 1.95 50 78248 3852 99.8 0.166 0.165 0.1736 0.186 0.1729 RANDOM 24.41
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] 0.38 0.38 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.357 r_dihedral_angle_3_deg 13.512 r_dihedral_angle_4_deg 13.469 r_dihedral_angle_1_deg 5.245 r_scangle_it 3.125 r_scbond_it 1.82 r_angle_other_deg 1.189 r_angle_refined_deg 1.095 r_mcangle_it 1.049 r_mcbond_it 0.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.357 r_dihedral_angle_3_deg 13.512 r_dihedral_angle_4_deg 13.469 r_dihedral_angle_1_deg 5.245 r_scangle_it 3.125 r_scbond_it 1.82 r_angle_other_deg 1.189 r_angle_refined_deg 1.095 r_mcangle_it 1.049 r_mcbond_it 0.526 r_mcbond_other 0.106 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 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 6269 Nucleic Acid Atoms Solvent Atoms 779 Heterogen Atoms 2
Software Software Software Name Purpose MOSFLM data reduction DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction SCALA data scaling