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The structure of Nt.BspD6I nicking endonuclease with all cysteines mutated by serine residues at 0.19 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 2.86 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.867 α = 90 b = 93.059 β = 112.89 c = 76.58 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 2016-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.96862 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 1.93 47.45 99.7 0.129 7.1 3.7 57969
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 1.93 2 99.8 0.636 1.9 3.8
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 2EWF 1.93 19.55 54989 2837 99.44 0.20863 0.20712 0.2127 0.23927 0.2433 RANDOM 39.405
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] 1.01 -0.19 1 -1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.25 r_dihedral_angle_4_deg 21.135 r_dihedral_angle_3_deg 16.853 r_long_range_B_refined 11.073 r_dihedral_angle_1_deg 6.627 r_mcangle_it 5.929 r_scbond_it 5.873 r_mcbond_it 4.325 r_angle_refined_deg 2.032 r_chiral_restr 0.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.25 r_dihedral_angle_4_deg 21.135 r_dihedral_angle_3_deg 16.853 r_long_range_B_refined 11.073 r_dihedral_angle_1_deg 6.627 r_mcangle_it 5.929 r_scbond_it 5.873 r_mcbond_it 4.325 r_angle_refined_deg 2.032 r_chiral_restr 0.147 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 4837 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction iMOSFLM data reduction SCALA data scaling MOLREP phasing