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Nuclease NucB from Bacillus licheniformis mutant N117Q
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EJV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 protein concentration was 18 mg/ml;
storage buffer: 20mM Tris pH 8.0, 100mM NaCl;
reservoir solution: 0.1 M 1,6-Hexanediol 0.1 M 1-Butanol 0.1 M 1,2-Propanediol 0.1 M 2-Propanol 0.1 M 1,4-Butanediol 0.1 M 1,3-Propanediol 0.85 M Tris and Bicine pH 8.5 10.5 % v/v 2-Methyl- -2,4,-pentanediol 10.5 % PEG 1000 10.5 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.92 57.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.497 α = 90 b = 53.497 β = 90 c = 84.596 γ = 120
Symmetry Space Group P 31 2 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 PIXEL DECTRIS PILATUS 6M 2021-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.25 46.33 100 0.067 0.071 0.023 0.998 22.4 9.5 39455 12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 100 1.659 1.752 0.556 0.659 1.7 9.7
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 (All) 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 1.25 46.33 39411 2002 99.894 0.129 0.12909 0.12549 0.1281 0.16305 0.1475 Random 17.64
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] 0.032 0.016 0.032 -0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.161 r_dihedral_angle_4_deg 18.674 r_dihedral_angle_3_deg 12.015 r_dihedral_angle_1_deg 6.072 r_rigid_bond_restr 4.414 r_lrange_it 3.734 r_lrange_other 3.331 r_scangle_it 3.057 r_scangle_other 3.055 r_scbond_it 2.542
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.161 r_dihedral_angle_4_deg 18.674 r_dihedral_angle_3_deg 12.015 r_dihedral_angle_1_deg 6.072 r_rigid_bond_restr 4.414 r_lrange_it 3.734 r_lrange_other 3.331 r_scangle_it 3.057 r_scangle_other 3.055 r_scbond_it 2.542 r_scbond_other 2.54 r_mcangle_other 2.218 r_mcangle_it 2.217 r_angle_refined_deg 1.825 r_mcbond_it 1.792 r_mcbond_other 1.698 r_angle_other_deg 1.671 r_nbd_refined 0.234 r_symmetry_nbd_other 0.203 r_nbd_other 0.184 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.172 r_symmetry_nbd_refined 0.163 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.009 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 844 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building