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Crystal structure of Enolase from Synechococcus elongatus, complex with phosphoenolpyruvate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E9I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 10-15% PEG200, 150-200mM CaAcetate, 0.1M Hepes pH 7.5, 10mM PEP
Crystal Properties Matthews coefficient Solvent content 2.73 55.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.23 α = 90 b = 164.23 β = 90 c = 72.68 γ = 90
Symmetry Space Group P 4 21 2
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 RAYONIX MX-300 2015-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-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 2.2 82.11 98.4 0.2 0.242 0.08 0.982 6.7 8.8 50150
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 2.2 2.27 84.6 0.36 6.1
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 1e9i 2.3 73.55 42379 2189 99.7 0.21449 0.21288 0.2228 0.24494 0.2513 RANDOM 30.054
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] -2.04 -2.04 4.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.362 r_dihedral_angle_4_deg 18.876 r_dihedral_angle_3_deg 15.014 r_dihedral_angle_1_deg 6.823 r_long_range_B_refined 5.551 r_long_range_B_other 5.543 r_scangle_other 4.345 r_mcangle_it 3.489 r_mcangle_other 3.488 r_scbond_it 2.761
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.362 r_dihedral_angle_4_deg 18.876 r_dihedral_angle_3_deg 15.014 r_dihedral_angle_1_deg 6.823 r_long_range_B_refined 5.551 r_long_range_B_other 5.543 r_scangle_other 4.345 r_mcangle_it 3.489 r_mcangle_other 3.488 r_scbond_it 2.761 r_scbond_other 2.76 r_mcbond_it 2.339 r_mcbond_other 2.332 r_angle_refined_deg 1.574 r_angle_other_deg 1.327 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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 6278 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing