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Crystal structure of Staphylococcal nuclease variant Delta+PHS T41V/S59A 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 7 277 35% MPD, 25 mM Potassium Phosphate,
Crystal Properties Matthews coefficient Solvent content 2.24 45.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.021 α = 90 b = 60.753 β = 92.92 c = 38.429 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 PIXEL RIGAKU HyPix-6000HE 2023-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU PhotonJet-R 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 2 21.92 99.9 0.013 0.086 76.43 10.4 9707 20.71
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 2 2.07 100 0.094 0.208 11.37 10.1
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 (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 2 21.7 9232 461 99.9 0.1872 0.18491 0.1931 0.2324 0.2411 RANDOM 31.448
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] -1.48 0.43 -0.28 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.451 r_long_range_B_refined 8.521 r_long_range_B_other 8.518 r_scangle_other 6.463 r_dihedral_angle_1_deg 6.326 r_dihedral_angle_2_deg 5.597 r_mcangle_other 4.372 r_mcangle_it 4.353 r_scbond_it 4.331 r_scbond_other 4.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.451 r_long_range_B_refined 8.521 r_long_range_B_other 8.518 r_scangle_other 6.463 r_dihedral_angle_1_deg 6.326 r_dihedral_angle_2_deg 5.597 r_mcangle_other 4.372 r_mcangle_it 4.353 r_scbond_it 4.331 r_scbond_other 4.327 r_mcbond_other 3.211 r_mcbond_it 3.21 r_angle_refined_deg 1.772 r_angle_other_deg 0.593 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 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 1032 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement CrysalisPro data scaling CrysalisPro data reduction PHASER phasing