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SmNuc1 nuclease from Stenotrophomonas maltophilia in complex with uridine - 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 0.1 M MES pH 6.5, 30 % w/v PEG 8000, 0.2 M Lithium sulfate. Protein concentration 11.8 mg/ml. Cryo-protection by glycerol 20 % v/v.
Crystal Properties Matthews coefficient Solvent content 2.34 47.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.434 α = 90 b = 72.8 β = 102.302 c = 82.928 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 2M 2022-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
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 1.2 43.41 97 0.081 0.09 0.998 11.5 5.1 155893 11.5
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 1.2 1.22 94 1.088 1.352 0.579 1.4 5.1
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 1.2 43.41 155884 7501 96.934 0.137 0.1369 0.1339 0.1361 0.1669 0.1447 random 20.454
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] 1.358 0.578 -1.124 -0.444
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.697 r_dihedral_angle_4_deg 18.558 r_dihedral_angle_3_deg 12.436 r_dihedral_angle_1_deg 6.121 r_lrange_it 3.82 r_lrange_other 3.442 r_scangle_other 3.274 r_scangle_it 3.267 r_rigid_bond_restr 3.105 r_scbond_it 2.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.697 r_dihedral_angle_4_deg 18.558 r_dihedral_angle_3_deg 12.436 r_dihedral_angle_1_deg 6.121 r_lrange_it 3.82 r_lrange_other 3.442 r_scangle_other 3.274 r_scangle_it 3.267 r_rigid_bond_restr 3.105 r_scbond_it 2.835 r_scbond_other 2.822 r_mcangle_it 2.107 r_mcangle_other 2.099 r_mcbond_it 1.785 r_mcbond_other 1.776 r_angle_other_deg 1.573 r_angle_refined_deg 1.56 r_nbd_other 0.248 r_nbd_refined 0.228 r_symmetry_nbd_other 0.182 r_symmetry_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.156 r_symmetry_xyhbond_nbd_other 0.131 r_symmetry_nbd_refined 0.12 r_chiral_restr 0.098 r_metal_ion_refined 0.091 r_symmetry_nbtor_other 0.081 r_xyhbond_nbd_other 0.034 r_symmetry_metal_ion_refined 0.017 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3857 Nucleic Acid Atoms Solvent Atoms 721 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing Coot model building