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Structure of E.coli enolase in complex with an analog of the natural product SF-2312 metabolite.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6D3Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 2.1 M Ammonium Sulfate,
0.1 M MES buffer pH 6.0,
0.2 M Sodium/Potassium tartrate
Crystal Properties Matthews coefficient Solvent content 2.26 45.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.18 α = 90 b = 143.11 β = 90 c = 206.679 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 325 mm CCD Mirror: Flat bent collimating Rh coated mirror, toroidal focussing mirror 2018-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.19499 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.57 93.03 99.4 0.075 0.106 0.075 0.984 5.9 1.9 97620 35.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.57 2.62 92.9 0.396 0.56 0.396 0.791 0.7 2
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 6D3Q 2.57 93.03 92667 4924 99.1 0.19383 0.19052 0.1996 0.25646 0.2615 RANDOM 47.153
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] 3.68 1.6 -5.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.295 r_dihedral_angle_4_deg 18.797 r_dihedral_angle_3_deg 15.858 r_long_range_B_refined 7.728 r_long_range_B_other 7.728 r_dihedral_angle_1_deg 7.562 r_scangle_other 5.536 r_mcangle_it 5.351 r_mcangle_other 5.351 r_scbond_it 3.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.295 r_dihedral_angle_4_deg 18.797 r_dihedral_angle_3_deg 15.858 r_long_range_B_refined 7.728 r_long_range_B_other 7.728 r_dihedral_angle_1_deg 7.562 r_scangle_other 5.536 r_mcangle_it 5.351 r_mcangle_other 5.351 r_scbond_it 3.59 r_scbond_other 3.59 r_mcbond_it 3.535 r_mcbond_other 3.535 r_angle_refined_deg 1.599 r_angle_other_deg 1.229 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 19325 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 151
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing