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Structure of E. coli ExoIX in complex with the palindromic 5ov4 DNA oligonucleotide, potassium and calcium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other EXOIX FLAP1 FRAGMENT COMPLEX STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.2 M CALCIUM ACETATE, 15% (W/V) PEG-3350, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.74 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.178 α = 90 b = 152.688 β = 90 c = 34.53 γ = 90
Symmetry Space Group P 21 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 ADSC QUANTUM 315 MIRRORS 2009-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.53 40 97.9 0.06 13.7 4.2 53386 6
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 1.53 1.61 97.9 0.42 3.2 3.4
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 EXOIX FLAP1 FRAGMENT COMPLEX STRUCTURE 1.53 34.53 50688 2697 99.2 0.20603 0.20485 0.2084 0.22865 0.2286 RANDOM 24.24
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] -0.64 0.47 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.585 r_scangle_it 17.688 r_scbond_it 16.671 r_dihedral_angle_4_deg 15.039 r_dihedral_angle_3_deg 11.732 r_mcangle_it 11.026 r_mcbond_it 9.593 r_dihedral_angle_1_deg 5.531 r_angle_refined_deg 1.429 r_mcbond_other 1.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.585 r_scangle_it 17.688 r_scbond_it 16.671 r_dihedral_angle_4_deg 15.039 r_dihedral_angle_3_deg 11.732 r_mcangle_it 11.026 r_mcbond_it 9.593 r_dihedral_angle_1_deg 5.531 r_angle_refined_deg 1.429 r_mcbond_other 1.019 r_angle_other_deg 0.931 r_chiral_restr 0.086 r_bond_refined_d 0.013 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1897 Nucleic Acid Atoms 245 Solvent Atoms 159 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling