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Crystal Structure of Beta-ketoacyl-ACP synthase III-2 (FabH2) (C113A) from Vibrio Cholerae co-crystallized with octanoyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WZU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 0.1M HEPES PH 7.5, 30% (W/V) PEG 400
Crystal Properties Matthews coefficient Solvent content 2.56 51.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.317 α = 90 b = 61.887 β = 93.18 c = 75.734 γ = 90
Symmetry Space Group P 1 21 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 210r 2015-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1.2861 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.16 50.01 99.3 0.057 0.037 38 3.2 42343
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.16 2.2 98.5 0.13 0.094 0.977 12 2.6
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 4WZU 2.16 50.01 40220 2042 99.22 0.17543 0.17385 0.1862 0.2066 0.212 RANDOM 41.065
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] -1.75 -0.08 -0.64 2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.964 r_dihedral_angle_4_deg 17.463 r_dihedral_angle_3_deg 11.951 r_dihedral_angle_1_deg 6.44 r_long_range_B_refined 4.629 r_long_range_B_other 4.629 r_scangle_other 1.667 r_angle_refined_deg 1.42 r_mcangle_it 1.156 r_mcangle_other 1.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.964 r_dihedral_angle_4_deg 17.463 r_dihedral_angle_3_deg 11.951 r_dihedral_angle_1_deg 6.44 r_long_range_B_refined 4.629 r_long_range_B_other 4.629 r_scangle_other 1.667 r_angle_refined_deg 1.42 r_mcangle_it 1.156 r_mcangle_other 1.156 r_scbond_it 1.023 r_scbond_other 1.023 r_angle_other_deg 0.933 r_mcbond_it 0.706 r_mcbond_other 0.704 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5348 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing