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SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with adenosine-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 6.5 291 0.2 M Ammonium sulfate 0.1 M MES pH 6.5, 30% w/v Polyethylene glycol 8000. Protein concentration 8.5 mg/ml. Cryo-protection by glycerol 20 % v/v.
Crystal Properties Matthews coefficient Solvent content 2.33 47.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.47 α = 90 b = 72.741 β = 102.684 c = 82.752 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 2021-10-15 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 1.65 43.385 88.8 0.105 0.113 0.998 13.2 6.9 52701
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 1.65 1.69 92.8 0.869 0.935 0.777 2.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.65 43.385 52701 2536 85.069 0.176 0.1759 0.1747 0.2143 0.1689 Random 19.032
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] 0.156 0.37 -0.33 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.664 r_dihedral_angle_4_deg 21.353 r_dihedral_angle_3_deg 14.055 r_dihedral_angle_1_deg 6.339 r_lrange_it 6.143 r_lrange_other 5.816 r_scangle_it 3.895 r_scangle_other 3.862 r_mcangle_it 2.561 r_mcangle_other 2.555
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.664 r_dihedral_angle_4_deg 21.353 r_dihedral_angle_3_deg 14.055 r_dihedral_angle_1_deg 6.339 r_lrange_it 6.143 r_lrange_other 5.816 r_scangle_it 3.895 r_scangle_other 3.862 r_mcangle_it 2.561 r_mcangle_other 2.555 r_scbond_it 2.535 r_scbond_other 2.461 r_mcbond_it 1.631 r_mcbond_other 1.622 r_angle_refined_deg 1.569 r_angle_other_deg 1.469 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.203 r_nbd_other 0.184 r_symmetry_nbd_other 0.181 r_symmetry_xyhbond_nbd_refined 0.165 r_nbtor_refined 0.164 r_symmetry_nbd_refined 0.154 r_symmetry_xyhbond_nbd_other 0.144 r_chiral_restr 0.086 r_metal_ion_refined 0.081 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3809 Nucleic Acid Atoms Solvent Atoms 589 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling MOLREP phasing Coot model building