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Crystal structure of Staphylococcal nuclease variant Delta+PHS V23D/L36K 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 20% MPD, 25 mM Potassium Phosphate,
Crystal Properties Matthews coefficient Solvent content 2.23 44.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.081 α = 90 b = 60.256 β = 94.75 c = 38.731 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 2020-10-21 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 1.9 23.73 99.9 0.017 0.041 53.12 10.1 11317 20.01
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 1.9 1.97 100 0.146 0.25 4.81 6.6
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 1.9 23.26 10751 545 99.93 0.19084 0.18924 0.1978 0.2224 0.2323 RANDOM 30.153
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] -1.1 0.47 -1.4 2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.658 r_long_range_B_refined 7.885 r_long_range_B_other 7.875 r_dihedral_angle_2_deg 7.44 r_dihedral_angle_1_deg 5.968 r_scangle_other 5.769 r_mcangle_it 3.805 r_mcangle_other 3.803 r_scbond_it 3.707 r_scbond_other 3.704
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.658 r_long_range_B_refined 7.885 r_long_range_B_other 7.875 r_dihedral_angle_2_deg 7.44 r_dihedral_angle_1_deg 5.968 r_scangle_other 5.769 r_mcangle_it 3.805 r_mcangle_other 3.803 r_scbond_it 3.707 r_scbond_other 3.704 r_mcbond_it 2.732 r_mcbond_other 2.732 r_angle_refined_deg 1.703 r_angle_other_deg 0.552 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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 1035 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement CrysalisPro data scaling CrysalisPro data reduction PHASER phasing