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Modification dependent TagI restriction endonuclease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CLZ 3clz, 5mkw experimental model PDB 5MKW 3clz, 5mkw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 7.5 294 A5 Morpheus Buffer
(10% w/v PEG 20 000, 20% v/v PEG MME 550,
0.03 M MgCl2, 0.03 M CaCl2, 0.1 M MOPS/HEPES-Na pH 7.5)
Crystal Properties Matthews coefficient Solvent content 4.4 72.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.963 α = 90 b = 72.963 β = 90 c = 207.576 γ = 90
Symmetry Space Group P 41 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 294 CCD Bruker Platinum 135 HELIOS multilayer optics 2018-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER X8 PROTEUM 1.54
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 2.92 20 96.1 0.2386 0.2196 4.38 3.23 12496
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 2.92 3.02 96.2 0.6983 0.9485 1.2 3.3
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 3clz, 5mkw 2.92 20 11890 607 96.64 0.19389 0.19242 0.1958 0.22309 0.2276 RANDOM 51.062
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] 1.54 1.54 -3.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.393 r_dihedral_angle_4_deg 21.054 r_dihedral_angle_3_deg 14.906 r_long_range_B_refined 7.486 r_long_range_B_other 7.481 r_dihedral_angle_1_deg 6.271 r_scangle_other 4.741 r_mcangle_it 4.623 r_mcangle_other 4.622 r_mcbond_it 2.689
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.393 r_dihedral_angle_4_deg 21.054 r_dihedral_angle_3_deg 14.906 r_long_range_B_refined 7.486 r_long_range_B_other 7.481 r_dihedral_angle_1_deg 6.271 r_scangle_other 4.741 r_mcangle_it 4.623 r_mcangle_other 4.622 r_mcbond_it 2.689 r_mcbond_other 2.684 r_scbond_other 2.675 r_scbond_it 2.674 r_angle_refined_deg 1.338 r_angle_other_deg 0.932 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 2212 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data reduction SAINT data scaling SADABS data scaling PHASER phasing FFFEAR phasing BALBES phasing BUCCANEER model building ARP/wARP model building