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The structure of yeast delta3-delta2-enoyl-COA isomerase complexed with octanoyl-COA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HNU PDB ENTRY 1HNU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 0.1 M TEA, 1.3 M sodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.87 68.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.65 α = 90 b = 116.65 β = 90 c = 216.78 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 IMAGE PLATE MARRESEARCH 2000-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 0.946 MAX II I711
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 3.3 20 0.131 7.5 5.3 23549 22527
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 3.3 3.42 96.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1HNU 3.29 20 21372 21512 1162 96.9 0.208 0.20508 0.1804 0.26209 RANDOM 19.628
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] -0.21 -0.21 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.398 r_scangle_it 2.097 r_angle_refined_deg 1.201 r_scbond_it 1.186 r_mcangle_it 0.887 r_mcbond_it 0.45 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.141 r_symmetry_hbond_refined 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.398 r_scangle_it 2.097 r_angle_refined_deg 1.201 r_scbond_it 1.186 r_mcangle_it 0.887 r_mcbond_it 0.45 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.141 r_symmetry_hbond_refined 0.129 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6399 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 186
Software Software Software Name Purpose DENZO data reduction TRUNCATE data reduction AMoRE phasing REFMAC refinement CCP4 data scaling