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Crystal structure of Staphylococcal nuclease variant Delta+PHS I72K L103K 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 20% MPD, 25 mM potassium phosphate, calcium chloride, pdTp
Crystal Properties Matthews coefficient Solvent content 2.31 46.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.12 α = 90 b = 61.64 β = 90 c = 80.399 γ = 90
Symmetry Space Group P 21 21 21
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 2016-05-06 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 1.83 50 99.9 0.057 60.29 19.4 13844 19.6
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 1.83 1.9 100 0.221 13.35 13.6
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 1.83 48.92 13080 720 99.94 0.19096 0.18849 0.1981 0.23744 0.2552 RANDOM 11.335
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.147 r_dihedral_angle_3_deg 15.848 r_dihedral_angle_4_deg 10.208 r_dihedral_angle_1_deg 6.069 r_long_range_B_refined 4.417 r_long_range_B_other 4.416 r_scangle_other 3.127 r_scbond_it 1.95 r_scbond_other 1.948 r_angle_refined_deg 1.813
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.147 r_dihedral_angle_3_deg 15.848 r_dihedral_angle_4_deg 10.208 r_dihedral_angle_1_deg 6.069 r_long_range_B_refined 4.417 r_long_range_B_other 4.416 r_scangle_other 3.127 r_scbond_it 1.95 r_scbond_other 1.948 r_angle_refined_deg 1.813 r_mcangle_other 1.405 r_mcangle_it 1.403 r_mcbond_it 0.941 r_mcbond_other 0.923 r_angle_other_deg 0.897 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.001 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 98 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XPREP data reduction PHASER phasing PDB_EXTRACT data extraction CrysalisPro data reduction