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NlaIV restriction endonuclease
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 294 10 mg/ml of the enzyme in 15 % glycerol, 50 mM NaOH/HEPES pH 7,5, 50 mM KCl, 10 mM DTT and 5 mM CaCl2 was mixed in 1:1 ratio with double stranded DNA composed of the 5'-ATGGTACCTGC-3' and 5'-CAGGTACCATG-3' strands. The protein-DNA solutions were in turn mixed in 1:1 ratio with the precipitant solution containing 2 M NaCl and 100 mM citric acid, pH 5.
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.38 α = 90 b = 110.38 β = 90 c = 209.006 γ = 120
Symmetry Space Group P 62 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 MARRESEARCH BENT MIRROR 2008-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6
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 2.8 30 98.5 0.043 0.04 28.92 7.5 18997
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.97 98.6 1.052 0.986 1.72 7.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.8 29.72 18083 912 98.46 0.19245 0.19095 0.2003 0.22103 0.2197 RANDOM 115.889
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] 1.68 0.84 1.68 -5.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.834 r_dihedral_angle_4_deg 16.289 r_dihedral_angle_3_deg 13.639 r_long_range_B_refined 9.963 r_long_range_B_other 9.927 r_scangle_other 6.542 r_mcangle_it 6.427 r_mcangle_other 6.427 r_dihedral_angle_1_deg 5.289 r_mcbond_it 3.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.834 r_dihedral_angle_4_deg 16.289 r_dihedral_angle_3_deg 13.639 r_long_range_B_refined 9.963 r_long_range_B_other 9.927 r_scangle_other 6.542 r_mcangle_it 6.427 r_mcangle_other 6.427 r_dihedral_angle_1_deg 5.289 r_mcbond_it 3.825 r_mcbond_other 3.814 r_scbond_it 3.765 r_scbond_other 3.765 r_angle_refined_deg 1.083 r_angle_other_deg 0.849 r_chiral_restr 0.062 r_bond_refined_d 0.007 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2056 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling STARANISO data scaling autoSHARP phasing SHELXDE phasing SOLOMON phasing DM phasing PARROT phasing ARP/wARP model building BUCCANEER model building