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Crystal structure of Staphylococcal nuclease variant Delta+PHS A132S 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 7 277 25% MPD, 25 mM potassium phosphate, calcium chloride, THP
Crystal Properties Matthews coefficient Solvent content 2.22 44.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.11 α = 90 b = 60.6 β = 93.26 c = 38.09 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 2018-04-04 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 1.95 38.03 99.9 0.018 55.48 10.4 10374 31.4
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 1.95 2.02 100 0.133 6.55 6.8
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 1.95 23.71 9906 453 99.91 0.2141 0.2121 0.2175 0.2586 0.2681 RANDOM 25.901
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] -0.03 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.248 r_dihedral_angle_3_deg 18.675 r_dihedral_angle_4_deg 12.688 r_dihedral_angle_1_deg 6.859 r_angle_refined_deg 1.661 r_angle_other_deg 1.386 r_chiral_restr 0.063 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.248 r_dihedral_angle_3_deg 18.675 r_dihedral_angle_4_deg 12.688 r_dihedral_angle_1_deg 6.859 r_angle_refined_deg 1.661 r_angle_other_deg 1.386 r_chiral_restr 0.063 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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 54 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PHASER phasing PDB_EXTRACT data extraction CrysalisPro data reduction CrysalisPro data scaling