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N-terminal domain of modification dependent EcoKMcrA restriction endonuclease (NEco) in complex with C5mCGG target sequence
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GHC PDB ENTRY 6GHC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 NEco in the crystallization buffer (20 mM Tris-HCl, pH 8.0, 0.1 M NaCl, 1 mM EDTA, 2 mM DTT) was concentrated to 8.7 mg/ml and mixed in the 1:1.2 ratio with 10-mer TCAC5mCGGTTC oligonucleotide, annealed to its complementary GAAC5mCGTGA strand. Crystals were grown by mixing 1.8 ul of the protein-DNA mixture with 2.2 ul of the condition F1 of the PACT premier crystal screen (MDL) (0.2 M NaF, 0.1 M Bis-Tris propane, pH 6.5, 20% PEG3350). Crystals were cryo-protected by the addition of 25% glycerol.
Crystal Properties Matthews coefficient Solvent content 8.29 85.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.432 α = 90 b = 112.432 β = 90 c = 155.457 γ = 120
Symmetry Space Group P 61 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 PIXEL DECTRIS PILATUS 6M 2018-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91840 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 2.64 45.55 99.8 0.223 0.23 0.997 12.52 16 17671 50.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.64 2.8 99.2 1.463 1.509 0.764 1.97 16.7
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 PDB ENTRY 6GHC 2.64 45.55 16786 884 99.82 0.19237 0.19052 0.1939 0.22921 0.2383 RANDOM 53.738
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] -1.73 -0.87 -1.73 5.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.592 r_dihedral_angle_4_deg 18.898 r_dihedral_angle_3_deg 12.424 r_dihedral_angle_1_deg 5.38 r_long_range_B_refined 4.943 r_long_range_B_other 4.915 r_scangle_other 3.299 r_mcangle_it 2.258 r_mcangle_other 2.257 r_scbond_it 1.894
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.592 r_dihedral_angle_4_deg 18.898 r_dihedral_angle_3_deg 12.424 r_dihedral_angle_1_deg 5.38 r_long_range_B_refined 4.943 r_long_range_B_other 4.915 r_scangle_other 3.299 r_mcangle_it 2.258 r_mcangle_other 2.257 r_scbond_it 1.894 r_scbond_other 1.894 r_mcbond_it 1.306 r_mcbond_other 1.306 r_angle_refined_deg 1.146 r_angle_other_deg 1.048 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.002 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 2320 Nucleic Acid Atoms 812 Solvent Atoms 141 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing ARP/wARP model building