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High resolution structure of Thermus thermophilus enoyl-acyl carrier protein reductase NAD-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 20% (W/V) POLYETHYLENE GLYCOL 4000, 100 MM SODIUM CITRATE PH 5.4, 2 MM NAD
Crystal Properties Matthews coefficient Solvent content 2.2 44.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.27 α = 90 b = 107.8 β = 95.89 c = 85.98 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 CCD TOROIDAL FOCUSING MIRROR 2008-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.85 40 95.9 0.06 10.1 2.9 77770 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 1.85 1.95 89.2 0.41 2.2 2.5
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 1.86 39.75 76657 1098 95.87 0.18277 0.18199 0.1874 0.23926 0.2431 RANDOM 22.445
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 -2.35 -2.46 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.539 r_dihedral_angle_4_deg 14.824 r_dihedral_angle_3_deg 13.185 r_dihedral_angle_1_deg 5.948 r_scangle_it 3.791 r_scbond_it 2.214 r_angle_refined_deg 1.48 r_mcangle_it 1.48 r_angle_other_deg 1.016 r_mcbond_it 0.817
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.539 r_dihedral_angle_4_deg 14.824 r_dihedral_angle_3_deg 13.185 r_dihedral_angle_1_deg 5.948 r_scangle_it 3.791 r_scbond_it 2.214 r_angle_refined_deg 1.48 r_mcangle_it 1.48 r_angle_other_deg 1.016 r_mcbond_it 0.817 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.207 r_mcbond_other 0.183 r_nbd_other 0.175 r_symmetry_vdw_other 0.175 r_nbtor_refined 0.167 r_metal_ion_refined 0.154 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.135 r_chiral_restr 0.088 r_nbtor_other 0.081 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other 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 7695 Nucleic Acid Atoms Solvent Atoms 545 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing