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Crystal structure of enolase from Synechococcus elongatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E9I PDB entry 1E9I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 10-15% PEG200, 150-200 mM calcium acetate, 0.1 M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.85 56.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.282 α = 90 b = 164.282 β = 90 c = 75.5 γ = 90
Symmetry Space Group I 4 2 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 ADSC QUANTUM 315r 2014-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.127092 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.05 37.8 98.7 0.115 0.038 0.998 9 10.1 30631
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.1 0.631 0.207 0.928 2.2
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 PDB entry 1E9I 2.05 37.78 30631 1561 98.74 0.20466 0.2031 0.2118 0.2342 0.2433 RANDOM 35.679
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] 0.07 0.07 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.686 r_dihedral_angle_4_deg 20.948 r_dihedral_angle_3_deg 15.069 r_dihedral_angle_1_deg 6.672 r_long_range_B_refined 6.513 r_long_range_B_other 6.5 r_scangle_other 5.71 r_scbond_it 3.897 r_scbond_other 3.896 r_mcangle_other 3.815
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.686 r_dihedral_angle_4_deg 20.948 r_dihedral_angle_3_deg 15.069 r_dihedral_angle_1_deg 6.672 r_long_range_B_refined 6.513 r_long_range_B_other 6.5 r_scangle_other 5.71 r_scbond_it 3.897 r_scbond_other 3.896 r_mcangle_other 3.815 r_mcangle_it 3.814 r_mcbond_it 3.092 r_mcbond_other 2.988 r_angle_refined_deg 1.632 r_angle_other_deg 1.395 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 3120 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing