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Crystal structure of Staphylococcal nuclease variant Delta+PHS F34Y at cryogenic temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BDC PDB entry 3BDC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 277 26% MPD, 25 mM potassium phosphate, calcium chloride, THP
Crystal Properties Matthews coefficient Solvent content 2.23 44.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.958 α = 90 b = 61.309 β = 92.98 c = 38.051 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 2018-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OTHER 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.1 38 99.9 0.021 41.1 10.6 8368 36.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 100 0.143 5.77 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB entry 3BDC 2.1 24.63 7937 417 99.94 0.2331 0.2306 0.2347 0.2791 0.2823 RANDOM 32.973
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] -0.07 -0.02 0.05 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.632 r_dihedral_angle_4_deg 18.37 r_dihedral_angle_3_deg 17.471 r_dihedral_angle_1_deg 6.592 r_angle_refined_deg 1.54 r_angle_other_deg 1.338 r_chiral_restr 0.055 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.632 r_dihedral_angle_4_deg 18.37 r_dihedral_angle_3_deg 17.471 r_dihedral_angle_1_deg 6.592 r_angle_refined_deg 1.54 r_angle_other_deg 1.338 r_chiral_restr 0.055 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1034 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PHASER phasing PDB_EXTRACT data extraction CrysalisPro data reduction CrysalisPro data scaling