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Crystal structure of enolase from E. coli with a mixture of apo form, substrate, and product form
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 2.9 57.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.262 α = 90 b = 143.293 β = 90 c = 207.04 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 PIXEL DECTRIS EIGER X 9M White beam slits, double crystal Si(111) monochromator with horizontal theta-axis, tandem flat beam deflecting silicon mirrors (Pd and Si lanes), Kirkpatrick-Baez focusing silica mirrors, Pd-coated, each bent adaptively with 16 piezo actuators 2017-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.979186 NSLS-II 17-ID-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 2.21 29.69 99.3 0.036 0.051 0.036 0.998 13.8 1.9 165432 30.4
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 2.21 2.24 87.4 0.332 0.47 0.332 0.786 2.2 1.9
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 2.21 29.69 156961 8374 99.26 0.17384 0.17148 0.1803 0.2182 0.2227 RANDOM 40.171
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] -0.2 2.12 -1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.416 r_dihedral_angle_4_deg 19.067 r_dihedral_angle_3_deg 14.741 r_long_range_B_other 7.702 r_long_range_B_refined 7.697 r_dihedral_angle_1_deg 7.003 r_scangle_other 6.522 r_mcangle_it 4.617 r_mcangle_other 4.617 r_scbond_it 4.508
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.416 r_dihedral_angle_4_deg 19.067 r_dihedral_angle_3_deg 14.741 r_long_range_B_other 7.702 r_long_range_B_refined 7.697 r_dihedral_angle_1_deg 7.003 r_scangle_other 6.522 r_mcangle_it 4.617 r_mcangle_other 4.617 r_scbond_it 4.508 r_scbond_other 4.508 r_mcbond_it 3.37 r_mcbond_other 3.368 r_angle_refined_deg 1.894 r_angle_other_deg 1.07 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19431 Nucleic Acid Atoms Solvent Atoms 676 Heterogen Atoms 167
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing