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Crystal structure of E. coli enolase complexed with the minimal binding segment of RNase E.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E9I Enolase structure 1E9I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 2.4M Sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K 2 VAPOR DIFFUSION, HANGING DROP 8.2 298 40% MPEG 550, 0.1M HEPES, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K 3 VAPOR DIFFUSION, HANGING DROP 6 298 8% PEG 4K, 0.2 M imidazole maleate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K 4 VAPOR DIFFUSION, HANGING DROP 7.5 298 27% PEG 600, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.054 α = 90 b = 124.201 β = 90.58 c = 96.076 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 315r 2004-05-08 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 210 2004-02-24 M SINGLE WAVELENGTH 3 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2004-03-09 M SINGLE WAVELENGTH 4 1 x-ray 100 CCD ADSC QUANTUM 4 2004-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 1.0 ESRF ID14-4 2 SYNCHROTRON ESRF BEAMLINE ID29 0.9782 ESRF ID29 3 ROTATING ANODE RIGAKU 1.54 4 SYNCHROTRON ESRF BEAMLINE ID14-4 1.0 ESRF ID14-4
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 1,2,3,4 1.6 20 91.1 0.034 13.7 10.3 216453 216432 2 2
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) 1.6 1.63 94.3 0.253 2.45 16.51
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Enolase structure 1E9I 1.6 19.99 216453 205585 10847 90.92 0.16652 0.16472 0.20102 0.2073 RANDOM 20.671
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] -0.02 -0.01 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.267 r_dihedral_angle_4_deg 18.674 r_dihedral_angle_3_deg 12.064 r_dihedral_angle_1_deg 5.413 r_sphericity_free 3.556 r_scangle_it 3.078 r_sphericity_bonded 2.843 r_scbond_it 2.697 r_rigid_bond_restr 2.495 r_mcangle_it 1.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.267 r_dihedral_angle_4_deg 18.674 r_dihedral_angle_3_deg 12.064 r_dihedral_angle_1_deg 5.413 r_sphericity_free 3.556 r_scangle_it 3.078 r_sphericity_bonded 2.843 r_scbond_it 2.697 r_rigid_bond_restr 2.495 r_mcangle_it 1.237 r_angle_refined_deg 1.157 r_mcbond_it 0.844 r_nbtor_refined 0.302 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.171 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12873 Nucleic Acid Atoms Solvent Atoms 1930 Heterogen Atoms 4
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction