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SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with guanosine-5'-monophosphate as a product of c-di-GMP cleavage
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QJL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 0.2 M Ammonium sulfate, 0.1 M MES pH 6.5, 30% w/v Polyethylene glycol 5000. Protein concentration 7.5 mg/ml. Cryo-protection by glycerol 25 % v/v.
Crystal Properties Matthews coefficient Solvent content 2.3 46.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.34 α = 90 b = 72.637 β = 102.098 c = 82.94 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 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) 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 1.148 43.393 96.8 0.045 0.054 1 18.5 6.6 165597
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.148 1.182 0.567 0.701 0.824 2.8
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.148 43.393 165597 7969 90.609 0.113 0.1129 0.1107 0.1275 0.1311 0.1266 15.231
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] 0.218 0.075 -0.319 0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.984 r_dihedral_angle_4_deg 17.464 r_dihedral_angle_other_3_deg 15.08 r_dihedral_angle_3_deg 13.027 r_dihedral_angle_1_deg 5.936 r_lrange_it 3.589 r_lrange_other 2.768 r_scangle_it 2.679 r_scangle_other 2.654 r_rigid_bond_restr 2.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.984 r_dihedral_angle_4_deg 17.464 r_dihedral_angle_other_3_deg 15.08 r_dihedral_angle_3_deg 13.027 r_dihedral_angle_1_deg 5.936 r_lrange_it 3.589 r_lrange_other 2.768 r_scangle_it 2.679 r_scangle_other 2.654 r_rigid_bond_restr 2.237 r_scbond_it 2.228 r_scbond_other 2.218 r_mcangle_it 1.799 r_mcangle_other 1.799 r_angle_refined_deg 1.606 r_angle_other_deg 1.579 r_mcbond_it 1.44 r_mcbond_other 1.426 r_xyhbond_nbd_other 0.242 r_nbd_other 0.231 r_nbd_refined 0.23 r_symmetry_nbd_refined 0.221 r_symmetry_xyhbond_nbd_refined 0.218 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.156 r_symmetry_metal_ion_refined 0.107 r_chiral_restr 0.104 r_symmetry_nbtor_other 0.084 r_metal_ion_refined 0.051 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3872 Nucleic Acid Atoms Solvent Atoms 747 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling MOLREP phasing Coot model building