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SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with guanosine-5'-monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QJL D_1292131829
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 0.2 M Lithium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3350, protein concentration 7.5 mg/ml. Cryo-protection by glycerol 20 % v/v.
Crystal Properties Matthews coefficient Solvent content 2.22 44.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.178 α = 90 b = 73.068 β = 105.324 c = 81.607 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 2020-11-20 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 1.85 41.64 96.4 0.129 0.152 0.994 7.1 3.5 40335 19.2
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 1.85 1.89 99.3 1.295 1.523 0.376 1.1
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 FREE R-VALUE 1.85 41.64 40318 2029 96.312 0.172 0.1723 0.1714 0.1805 0.2091 0.1845 Random 27.984
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] 1.471 0.222 -1.479 -0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.346 r_dihedral_angle_4_deg 17.843 r_dihedral_angle_3_deg 14.532 r_dihedral_angle_1_deg 6.625 r_lrange_it 6.254 r_lrange_other 6.155 r_scangle_it 4.41 r_scangle_other 4.343 r_mcangle_it 3.276 r_mcangle_other 3.276
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.346 r_dihedral_angle_4_deg 17.843 r_dihedral_angle_3_deg 14.532 r_dihedral_angle_1_deg 6.625 r_lrange_it 6.254 r_lrange_other 6.155 r_scangle_it 4.41 r_scangle_other 4.343 r_mcangle_it 3.276 r_mcangle_other 3.276 r_scbond_it 2.809 r_scbond_other 2.686 r_mcbond_it 2.099 r_mcbond_other 2.099 r_angle_refined_deg 1.445 r_angle_other_deg 1.339 r_symmetry_nbd_refined 0.232 r_nbd_other 0.228 r_nbd_refined 0.215 r_symmetry_nbd_other 0.179 r_xyhbond_nbd_refined 0.165 r_nbtor_refined 0.157 r_symmetry_xyhbond_nbd_refined 0.125 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.075 r_metal_ion_refined 0.075 r_symmetry_xyhbond_nbd_other 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3842 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms 197
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing Coot model building