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Yeast enoyl-CoA isomerase (ScECI2) complexed with acetoacetyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K39
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 100 mM MES pH 6.5,
1.6 M (NH4)2SO4,
10% dioxane
Crystal Properties Matthews coefficient Solvent content 3.7 66.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.937 α = 90 b = 116.937 β = 90 c = 218.632 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 273 PIXEL PSI PILATUS 6M 2013-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.945 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.14 103.1 99.5 0.122 14 14.3 83764
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 2.14 2.18 91.1 0.802 2 6.1
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 1k39 2.14 103.1 79476 4184 99.52 0.16613 0.16487 0.1747 0.19013 0.1981 RANDOM 40.968
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] -0.25 -0.25 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.714 r_dihedral_angle_4_deg 15.613 r_dihedral_angle_3_deg 15.142 r_long_range_B_refined 8.136 r_long_range_B_other 8.136 r_scangle_other 6.239 r_dihedral_angle_1_deg 5.245 r_scbond_it 4.189 r_scbond_other 4.189 r_mcangle_it 4.037
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.714 r_dihedral_angle_4_deg 15.613 r_dihedral_angle_3_deg 15.142 r_long_range_B_refined 8.136 r_long_range_B_other 8.136 r_scangle_other 6.239 r_dihedral_angle_1_deg 5.245 r_scbond_it 4.189 r_scbond_other 4.189 r_mcangle_it 4.037 r_mcangle_other 4.037 r_mcbond_it 2.827 r_mcbond_other 2.826 r_angle_refined_deg 1.717 r_angle_other_deg 1.088 r_chiral_restr 0.106 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6306 Nucleic Acid Atoms Solvent Atoms 411 Heterogen Atoms 244
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing