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SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with cytidine - 5' - monophosphate as an inhibitor.
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 0.1 M Bis-Tris pH 5.5, 25 % w/v PEG 3350, 0.2 M Lithium sulfate, cryo-protection 25% v/v glycerol, protein concentration 7.5 mg/ml.
Crystal Properties Matthews coefficient Solvent content 2.23 44.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.255 α = 90 b = 73.166 β = 104.991 c = 81.66 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 1.8 41.78 99.4 0.108 0.117 0.995 14.2 6.7 45358 19.6
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 1.8 1.84 98.9 1.059 1.153 0.699 1.9 6.4
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 1.8 41.78 45328 2212 99.316 0.167 0.1675 0.1663 0.1788 0.2025 0.1808 Random 29.076
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] 1.031 -0.769 -1.087 0.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.218 r_dihedral_angle_4_deg 18.024 r_dihedral_angle_3_deg 13.754 r_dihedral_angle_other_3_deg 10.906 r_dihedral_angle_1_deg 6.613 r_lrange_it 6.477 r_lrange_other 6.241 r_scangle_it 4.053 r_scangle_other 3.932 r_mcangle_it 3.259
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.218 r_dihedral_angle_4_deg 18.024 r_dihedral_angle_3_deg 13.754 r_dihedral_angle_other_3_deg 10.906 r_dihedral_angle_1_deg 6.613 r_lrange_it 6.477 r_lrange_other 6.241 r_scangle_it 4.053 r_scangle_other 3.932 r_mcangle_it 3.259 r_mcangle_other 3.258 r_scbond_it 2.674 r_scbond_other 2.469 r_mcbond_it 2.114 r_mcbond_other 2.113 r_angle_refined_deg 1.408 r_angle_other_deg 1.351 r_nbd_other 0.232 r_symmetry_nbd_refined 0.23 r_nbd_refined 0.215 r_symmetry_xyhbond_nbd_refined 0.193 r_xyhbond_nbd_refined 0.187 r_symmetry_nbd_other 0.171 r_nbtor_refined 0.155 r_symmetry_xyhbond_nbd_other 0.084 r_symmetry_nbtor_other 0.076 r_metal_ion_refined 0.072 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.001 r_ext_dist_refined_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3890 Nucleic Acid Atoms Solvent Atoms 418 Heterogen Atoms 188
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing Coot model building