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SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with cytidine-5'-monophosphate
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, SITTING DROP 5.5 291 0.2 M Lithium sulfate 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350. Protein concentration 7.5 mg/ml. Cryo-protection by PEG400 30 % v/v.
Crystal Properties Matthews coefficient Solvent content 2.2 44.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.139 α = 90 b = 72.805 β = 105.066 c = 81.238 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 Bruker PHOTON II HELIOS MX, Ga 2019-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE Excillum MetalJet D2 70 kV 1.3418
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 41.66 99.2 0.124 0.149 0.961 6.8 3.2 57878
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 0.596 0.722 0.559
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 1.65 41.66 57816 2819 99.012 0.173 0.1732 0.1726 0.1856 0.1979 0.1861 Random 12.199
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] 1.178 -0.898 -0.499 -0.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.632 r_dihedral_angle_4_deg 18.296 r_dihedral_angle_3_deg 15.632 r_dihedral_angle_1_deg 6.379 r_lrange_it 4.912 r_lrange_other 4.547 r_scangle_other 2.755 r_scangle_it 2.75 r_scbond_it 1.734 r_scbond_other 1.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.632 r_dihedral_angle_4_deg 18.296 r_dihedral_angle_3_deg 15.632 r_dihedral_angle_1_deg 6.379 r_lrange_it 4.912 r_lrange_other 4.547 r_scangle_other 2.755 r_scangle_it 2.75 r_scbond_it 1.734 r_scbond_other 1.706 r_mcangle_other 1.661 r_mcangle_it 1.66 r_angle_refined_deg 1.607 r_angle_other_deg 1.474 r_mcbond_it 1.068 r_mcbond_other 1.064 r_nbd_other 0.234 r_nbd_refined 0.223 r_symmetry_nbd_refined 0.192 r_symmetry_xyhbond_nbd_refined 0.191 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.08 r_metal_ion_refined 0.066 r_symmetry_metal_ion_refined 0.052 r_symmetry_xyhbond_nbd_other 0.037 r_xyhbond_nbd_other 0.022 r_bond_refined_d 0.011 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 3880 Nucleic Acid Atoms Solvent Atoms 538 Heterogen Atoms 151
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing