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High resolution structure of Thermus thermophilus enoyl-acyl carrier protein reductase NAD and triclosan-form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WYU PDB ENTRY 2WYU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.4 32% (W/V) POLYETHYLENE GLYCOL 4000, 100 MM SODIUM CITRATE PH 5.4, 2 MM NAD, SOAKING FOR 48 HOURS IN 3.2 MM TRICLOSAN
Crystal Properties Matthews coefficient Solvent content 2.1 40.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.71 α = 90 b = 127.55 β = 108.2 c = 66.5 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 IMAGE PLATE MAR555 FLAT PANEL ELLIPTICALLY BENT 12 QUARTZ SEGMENTS 2009-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 1.9 30 91.2 0.07 10.5 3.5 65244 21.5
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 1.9 2 82.1 0.39 2.9 3.5
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 2WYU 1.9 27.93 62991 2198 99.92 0.1565 0.15507 0.1602 0.19561 0.1993 RANDOM 17.978
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] 0.83 -0.31 -0.61 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.359 r_dihedral_angle_4_deg 17.024 r_dihedral_angle_3_deg 12.13 r_dihedral_angle_1_deg 6.123 r_scangle_it 3.673 r_scbond_it 2.146 r_angle_refined_deg 1.461 r_mcangle_it 1.343 r_angle_other_deg 0.926 r_mcbond_it 0.732
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.359 r_dihedral_angle_4_deg 17.024 r_dihedral_angle_3_deg 12.13 r_dihedral_angle_1_deg 6.123 r_scangle_it 3.673 r_scbond_it 2.146 r_angle_refined_deg 1.461 r_mcangle_it 1.343 r_angle_other_deg 0.926 r_mcbond_it 0.732 r_symmetry_vdw_other 0.23 r_nbd_refined 0.208 r_nbd_other 0.182 r_nbtor_refined 0.178 r_symmetry_hbond_refined 0.172 r_mcbond_other 0.168 r_xyhbond_nbd_refined 0.151 r_symmetry_vdw_refined 0.151 r_nbtor_other 0.085 r_chiral_restr 0.081 r_xyhbond_nbd_other 0.081 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 7836 Nucleic Acid Atoms Solvent Atoms 675 Heterogen Atoms 244
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing