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beta-ketoacyl-ACP synthase I (KAS) from E. coli with bound amino- thiazole inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EK4 PDB ENTRY 1EK4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 CRYSTALLIZATION CONDITIONS: HANGING DROP AGAINST 3% PEG 400, 1.9 M AMMONIUM SULPHATE, 0.1 M TRIS PH 7.5 SOAK WITH 0.01M LIGAND IN 30% PEG8000, 0.1M AMMONIUM SULPHATE, 0.1M TRIS PH7.5, 0.005M TCEP
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.95 α = 90 b = 139.48 β = 90 c = 212.17 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH 2005-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 1.36 20 92.3 0.06 13.5 3 685131 5
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 1.35 1.45 72.9 0.2 6.2 2.7
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1EK4 1.36 19.87 337314 17776 94.5 0.121 0.119 0.1208 0.151 RANDOM 17.49
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] 0.07 0.37 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.461 r_dihedral_angle_4_deg 19.045 r_dihedral_angle_3_deg 12.162 r_dihedral_angle_1_deg 5.875 r_scangle_it 3.912 r_mcangle_it 3.184 r_scbond_it 2.876 r_mcbond_it 2.331 r_angle_refined_deg 1.581 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.461 r_dihedral_angle_4_deg 19.045 r_dihedral_angle_3_deg 12.162 r_dihedral_angle_1_deg 5.875 r_scangle_it 3.912 r_mcangle_it 3.184 r_scbond_it 2.876 r_mcbond_it 2.331 r_angle_refined_deg 1.581 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.211 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.175 r_symmetry_hbond_refined 0.171 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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_other r_long_range_B_refined 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 11768 Nucleic Acid Atoms Solvent Atoms 2431 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing