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Crystal structure of enolase from Escherichia coli with bound 2-phosphoglycerate substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FYM PDB entry 2FYM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 2.0 M ammonium sulfate, 0.1 M MES, pH 6.0, 0.1 M sodium/potassium tartrate
Crystal Properties Matthews coefficient Solvent content 2.74 55.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.94 α = 90 b = 142.4 β = 90 c = 206.64 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 2017-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.1949 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 1.81 78.61 100 0.116 0.132 0.062 0.991 6.1 4 283200 17.49
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 1.81 1.84 99.9 0.607 0.702 0.349 0.813 1.5 3.9
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 PDB entry 2FYM 1.81 78.61 269041 14046 99.92 0.16892 0.16562 0.1947 0.23223 0.2276 RANDOM 26.19
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] 1.68 0.92 -2.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.855 r_dihedral_angle_4_deg 17.431 r_sphericity_free 17.339 r_dihedral_angle_3_deg 14.479 r_sphericity_bonded 10.21 r_dihedral_angle_1_deg 6.915 r_scangle_other 5.124 r_scbond_it 4.763 r_scbond_other 4.758 r_long_range_B_refined 4.631
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.855 r_dihedral_angle_4_deg 17.431 r_sphericity_free 17.339 r_dihedral_angle_3_deg 14.479 r_sphericity_bonded 10.21 r_dihedral_angle_1_deg 6.915 r_scangle_other 5.124 r_scbond_it 4.763 r_scbond_other 4.758 r_long_range_B_refined 4.631 r_long_range_B_other 4.631 r_rigid_bond_restr 4.544 r_mcangle_it 3.938 r_mcangle_other 3.938 r_mcbond_it 3.563 r_mcbond_other 3.562 r_angle_refined_deg 2.231 r_angle_other_deg 1.18 r_chiral_restr 0.148 r_bond_refined_d 0.026 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19500 Nucleic Acid Atoms Solvent Atoms 1103 Heterogen Atoms 206
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing