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Crystal structure of E. coli Exonuclease I in complex with a dT13 oligonucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FXX PDB ENTRY 1FXX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 5% 2-propanol, 25 % glycerol, 1.2 M ammonium sulfate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.65 73.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.33 α = 90 b = 158.33 β = 90 c = 151.05 γ = 120
Symmetry Space Group P 31 2 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 RAYONIX MX225HE 2012-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
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 3.5 49 99.9 0.1 9.6 11 26653 26653 1 1
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 3.5 3.69 100 0.786 2 10.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 1FXX 3.5 49 1 1 2653 26653 1409 99.86 0.30815 0.30614 0.303 0.34642 0.3444 RANDOM 196.357
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] 1.96 1.96 1.96 -6.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.142 r_dihedral_angle_3_deg 14.951 r_dihedral_angle_4_deg 9.418 r_dihedral_angle_1_deg 5.526 r_angle_refined_deg 0.849 r_angle_other_deg 0.733 r_chiral_restr 0.051 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.142 r_dihedral_angle_3_deg 14.951 r_dihedral_angle_4_deg 9.418 r_dihedral_angle_1_deg 5.526 r_angle_refined_deg 0.849 r_angle_other_deg 0.733 r_chiral_restr 0.051 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 7431 Nucleic Acid Atoms 420 Solvent Atoms Heterogen Atoms 10
Software Software Software Name Purpose XDS data scaling AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling