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Crystal structure of yeast enoyl-CoA isomerase helix-10 deletion (ScECI2-H10) mutant
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 imidazole pH 6.5, 1 M NaAcetate
Crystal Properties Matthews coefficient Solvent content 2.7 54.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.121 α = 90 b = 118.121 β = 90 c = 87.417 γ = 120
Symmetry Space Group P 3 2 1
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 2014-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
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 1.81 48.94 99.7 0.073 17.3 10.5 64106
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 1.81 1.87 97.2 1.064 1.6 6.7
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 1.81 48.94 60869 3239 99.6 0.16062 0.15917 0.1722 0.18785 0.1979 RANDOM 35.875
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] -0.66 -0.33 -0.66 2.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.005 r_dihedral_angle_4_deg 18.784 r_dihedral_angle_3_deg 15.21 r_long_range_B_other 9.302 r_long_range_B_refined 9.3 r_scangle_other 5.771 r_dihedral_angle_1_deg 5.304 r_mcangle_it 3.698 r_mcangle_other 3.697 r_scbond_it 3.674
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.005 r_dihedral_angle_4_deg 18.784 r_dihedral_angle_3_deg 15.21 r_long_range_B_other 9.302 r_long_range_B_refined 9.3 r_scangle_other 5.771 r_dihedral_angle_1_deg 5.304 r_mcangle_it 3.698 r_mcangle_other 3.697 r_scbond_it 3.674 r_scbond_other 3.656 r_mcbond_it 2.497 r_mcbond_other 2.497 r_angle_refined_deg 1.464 r_angle_other_deg 0.992 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 4072 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing