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Apo structure of the 3-ketoacyl-CoA thiolase FadA5 from M. tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UBV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.1 293 0.1 M Mes pH 6.1, 5% DMSO, 1.8 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.73 54.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.25 α = 90 b = 128.25 β = 90 c = 114.01 γ = 90
Symmetry Space Group P 41 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 225 mm CCD 2012-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 2.7 52.02 94.4 0.143 11.8 7.6 25129
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.85 88.6 2.2 6.2
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 4ubv 2.7 51.29 23813 1264 93.72 0.17508 0.17112 0.1714 0.24808 0.2474 RANDOM 42.358
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] -1.52 -1.52 3.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.482 r_dihedral_angle_3_deg 18.477 r_dihedral_angle_4_deg 16.627 r_long_range_B_refined 7.448 r_dihedral_angle_1_deg 7.414 r_scbond_it 3.205 r_mcangle_it 3.034 r_mcbond_it 1.836 r_angle_refined_deg 1.695 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.482 r_dihedral_angle_3_deg 18.477 r_dihedral_angle_4_deg 16.627 r_long_range_B_refined 7.448 r_dihedral_angle_1_deg 7.414 r_scbond_it 3.205 r_mcangle_it 3.034 r_mcbond_it 1.836 r_angle_refined_deg 1.695 r_chiral_restr 0.109 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5724 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing