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Crystal structure of the ternary EcoRV-DNA-Lu complex with uncleaved DNA substrate. Lanthanide binding to EcoRV-DNA complex inhibits cleavage.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B95
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 285 4.5 mg/mL (monomer), protein(dimer):DNA - 1:1, Enzyme:Well - 3uL:3uL, Well - 500uL of 100 mM HEPES pH 7.4, 8% Ethylene glycol, 4% Polyethylene glycol 8000, 10% glycerol.
Crystal Properties Matthews coefficient Solvent content 2.24 45.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.43 α = 70.61 b = 52.86 β = 73.24 c = 65.31 γ = 81.81
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS HTC 2015-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.76 36.673 93 0.051 0.059 14.7 3.9 51697 21.698
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 1.76 1.85 88.9 0.196 4.4 3.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1B95 1.76 36.673 46685 5000 92.94 0.16402 0.16026 0.19914 0.2216 RANDOM 27.868
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] 0.96 -0.78 0.85 1.36 -0.66 -1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.752 r_dihedral_angle_4_deg 20.122 r_dihedral_angle_3_deg 14.434 r_dihedral_angle_1_deg 6.598 r_long_range_B_refined 6.468 r_long_range_B_other 6.468 r_scangle_other 5.393 r_scbond_it 3.806 r_scbond_other 3.806 r_mcangle_other 3.521
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.752 r_dihedral_angle_4_deg 20.122 r_dihedral_angle_3_deg 14.434 r_dihedral_angle_1_deg 6.598 r_long_range_B_refined 6.468 r_long_range_B_other 6.468 r_scangle_other 5.393 r_scbond_it 3.806 r_scbond_other 3.806 r_mcangle_other 3.521 r_mcangle_it 3.52 r_mcbond_it 2.672 r_mcbond_other 2.666 r_angle_refined_deg 1.574 r_angle_other_deg 1.056 r_chiral_restr 0.103 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 0.002 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 4046 Nucleic Acid Atoms 486 Solvent Atoms 301 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing