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Crystal structure of the ternary EcoRV-DNA-Lu complex with cleaved DNA substrate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B94
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 9.4 mg/mL, 3:3 Enzyme:Well, 100 mM HEPES pH 7.5, 8% Ethylene glycol, 7% Polyethylene glycol 8000, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 2.01 38.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.621 α = 96.94 b = 48.327 β = 108.78 c = 63.531 γ = 106.7
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 RIGAKU SATURN 944 2014-01-08 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) 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 1.95 58.46 78.9 0.051 0.057 0.995 20.3 4.3 28737 2 18.6
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 1.95 2 12 0.238 2.7 1.6
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 1B94 2 40 26617 1365 82.95 0.16858 0.16553 0.1771 0.22832 0.2324 RANDOM 22.437
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] 0.37 -1.03 -0.79 2.48 -0.25 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.576 r_dihedral_angle_4_deg 16.997 r_dihedral_angle_3_deg 15.107 r_dihedral_angle_1_deg 6.95 r_long_range_B_refined 6.616 r_long_range_B_other 6.614 r_scangle_other 4.002 r_mcangle_it 3.172 r_mcangle_other 3.171 r_scbond_it 2.463
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.576 r_dihedral_angle_4_deg 16.997 r_dihedral_angle_3_deg 15.107 r_dihedral_angle_1_deg 6.95 r_long_range_B_refined 6.616 r_long_range_B_other 6.614 r_scangle_other 4.002 r_mcangle_it 3.172 r_mcangle_other 3.171 r_scbond_it 2.463 r_scbond_other 2.46 r_mcbond_it 1.944 r_mcbond_other 1.944 r_angle_refined_deg 1.78 r_angle_other_deg 1.146 r_chiral_restr 0.116 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 468 Solvent Atoms 237 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing