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The structure of C160S,C508S,C578S mutant of Nt.BspD6I nicking endonuclease at 0.185 nm resolution .
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EWF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 16% PEG 8000
40MM POTASSIUM PHOSPHATE
20% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.81 56.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.204 α = 90 b = 92.485 β = 105.67 c = 113.808 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 315r MIRROR 2016-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97623 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.85 109.6 99.6 0.033 18.7 3.8 129563 2 34.15
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 1.85 1.92 99.6 0.66 2 3.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2EWF 1.85 19.58 122837 6247 99.54 0.21116 0.20915 0.25143 0.2613 RANDOM 48.377
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] -2.16 1.1 -0.63 1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.841 r_dihedral_angle_4_deg 18.528 r_dihedral_angle_3_deg 16.21 r_long_range_B_refined 10.794 r_scbond_it 6.434 r_dihedral_angle_1_deg 6.394 r_mcangle_it 5.847 r_mcbond_it 4.673 r_angle_refined_deg 1.943 r_chiral_restr 0.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.841 r_dihedral_angle_4_deg 18.528 r_dihedral_angle_3_deg 16.21 r_long_range_B_refined 10.794 r_scbond_it 6.434 r_dihedral_angle_1_deg 6.394 r_mcangle_it 5.847 r_mcbond_it 4.673 r_angle_refined_deg 1.943 r_chiral_restr 0.143 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9671 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement XDS data reduction iMOSFLM data reduction SCALA data scaling MOLREP phasing