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beta-ketoacyl-ACP synthase I (KAS) from E. coli with bound inhibitor thiolactomycin
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 0.3MM LIGAND IN 2.3M AMMONIUM SULPHATE, 0.1M TRIS PH7.5, 3% DMSO
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.139 α = 90 b = 138.345 β = 90 c = 211.968 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 2004-07-08 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 1.5 20 95.8 0.09 14.2 3.1 515847 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 1.5 1.6 78 0.43 3.51 2.68
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 PDB ENTRY 1EK4 1.52 119.52 253711 13446 99.3 0.153 0.151 0.1501 0.185 0.1832 RANDOM 16.85
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] 0.01 0.48 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.563 r_dihedral_angle_4_deg 17.164 r_dihedral_angle_3_deg 12.244 r_dihedral_angle_1_deg 5.898 r_scangle_it 4.564 r_scbond_it 3.183 r_mcangle_it 2.766 r_mcbond_it 2.215 r_angle_refined_deg 1.502 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.563 r_dihedral_angle_4_deg 17.164 r_dihedral_angle_3_deg 12.244 r_dihedral_angle_1_deg 5.898 r_scangle_it 4.564 r_scbond_it 3.183 r_mcangle_it 2.766 r_mcbond_it 2.215 r_angle_refined_deg 1.502 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.257 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.208 r_xyhbond_nbd_refined 0.196 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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 11748 Nucleic Acid Atoms Solvent Atoms 2645 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling