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Crystal structure of Staphylococcal nuclease variant Delta+PHS V23D/L36R at cryogenic temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BDC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 277 30% MPD, 25mM Potassium Phosphate
Crystal Properties Matthews coefficient Solvent content 2.22 44.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.172 α = 90 b = 60.277 β = 93.69 c = 38.35 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 110 CCD AGILENT ATLAS CCD 2021-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE Agilent SuperNova 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.85 23.66 99.9 0.024 0.083 36.95 10.3 12187 16.26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 100 0.161 0.256 4.91 6.5
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 (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 THROUGHOUT 1.85 23.42 11549 622 99.94 0.16836 0.16615 0.175 0.20887 0.2126 RANDOM 24.279
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] -0.49 0.29 -0.81 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.631 r_long_range_B_refined 6.385 r_long_range_B_other 6.239 r_dihedral_angle_2_deg 5.823 r_dihedral_angle_1_deg 5.809 r_scangle_other 4.879 r_scbond_it 3.081 r_scbond_other 3.078 r_mcangle_other 2.898 r_mcangle_it 2.894
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.631 r_long_range_B_refined 6.385 r_long_range_B_other 6.239 r_dihedral_angle_2_deg 5.823 r_dihedral_angle_1_deg 5.809 r_scangle_other 4.879 r_scbond_it 3.081 r_scbond_other 3.078 r_mcangle_other 2.898 r_mcangle_it 2.894 r_mcbond_it 1.942 r_mcbond_other 1.922 r_angle_refined_deg 1.598 r_angle_other_deg 0.566 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1037 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement CrysalisPro data scaling CrysalisPro data reduction PHASER phasing