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SmNuc1 nuclease from Stenotrophomonas maltophilia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FB9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 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 glycerol 20 % v/v.
Crystal Properties Matthews coefficient Solvent content 2.36 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.47 α = 90 b = 72.97 β = 90 c = 49.95 γ = 90
Symmetry Space Group P 21 21 2
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 2019-10-14 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 1.4 41.22 96 0.118 0.122 0.999 19.9 14.3 50815 8.9
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 1.4 1.42 98.1 1.166 1.32 0.509 4.3
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 1.4 41.22 50768 2516 95.923 0.123 0.1228 0.1186 0.122 0.1612 0.1376 Random 13.934
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] 0.242 -0.052 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.219 r_dihedral_angle_4_deg 18.013 r_dihedral_angle_other_3_deg 13.792 r_dihedral_angle_3_deg 11.907 r_dihedral_angle_1_deg 6.262 r_lrange_it 3.66 r_scangle_it 2.294 r_scangle_other 2.294 r_lrange_other 2.176 r_scbond_it 2.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.219 r_dihedral_angle_4_deg 18.013 r_dihedral_angle_other_3_deg 13.792 r_dihedral_angle_3_deg 11.907 r_dihedral_angle_1_deg 6.262 r_lrange_it 3.66 r_scangle_it 2.294 r_scangle_other 2.294 r_lrange_other 2.176 r_scbond_it 2.022 r_scbond_other 2.021 r_rigid_bond_restr 1.901 r_angle_refined_deg 1.692 r_angle_other_deg 1.612 r_mcangle_it 1.486 r_mcangle_other 1.486 r_mcbond_it 1.228 r_mcbond_other 1.19 r_xyhbond_nbd_other 0.46 r_nbd_refined 0.225 r_nbd_other 0.195 r_symmetry_nbd_other 0.18 r_symmetry_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.148 r_symmetry_nbd_refined 0.12 r_chiral_restr 0.115 r_symmetry_nbtor_other 0.085 r_metal_ion_refined 0.058 r_symmetry_xyhbond_nbd_other 0.036 r_bond_refined_d 0.011 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 1907 Nucleic Acid Atoms Solvent Atoms 455 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building Aimless data scaling