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Structure of yeast D3,D2-enoyl-CoA isomerase bound to sulphate ion
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 5.6 295 100 mM NaCitrate pH 5.6, 1 M (Li)2SO4, 500 mM (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 3.5 64.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.054 α = 90 b = 116.054 β = 90 c = 122.096 γ = 120
Symmetry Space Group P 63 2 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 DECTRIS PILATUS 6M 2015-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.920 Diamond I04-1
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 77.6 100 0.218 8.9 21.2 10249
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 3 3.18 100 1.342 2.2 22.8
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 3 40 9688 532 99.88 0.17491 0.17237 0.1829 0.22301 0.2257 RANDOM 62.586
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] -2.61 -1.3 -2.61 8.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.085 r_dihedral_angle_4_deg 19.473 r_dihedral_angle_3_deg 16.938 r_long_range_B_refined 10.894 r_long_range_B_other 10.604 r_scangle_other 8.206 r_dihedral_angle_1_deg 6.673 r_mcangle_other 6.493 r_mcangle_it 6.492 r_scbond_it 5.722
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.085 r_dihedral_angle_4_deg 19.473 r_dihedral_angle_3_deg 16.938 r_long_range_B_refined 10.894 r_long_range_B_other 10.604 r_scangle_other 8.206 r_dihedral_angle_1_deg 6.673 r_mcangle_other 6.493 r_mcangle_it 6.492 r_scbond_it 5.722 r_scbond_other 5.282 r_mcbond_it 4.341 r_mcbond_other 4.317 r_angle_refined_deg 1.608 r_angle_other_deg 0.799 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1968 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling