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Crystal structure of Staphylcoccal nuclease variant Delta+PHS I72K V74K 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, 25mM potassium phosphate, calcium chloride, pdTp
Crystal Properties Matthews coefficient Solvent content 2.17 43.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.88 α = 90 b = 59.889 β = 90 c = 73.765 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 APEX II CCD mirrors 2014-04-28 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 1.65 50 99.9 0.0185 47.22 35.43 17697 17697 21.6
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 1.65 1.67 98.6 0.2921 3.3 4.97
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 1.65 36.88 17640 894 99.89 0.183 0.1816 0.1923 0.21 0.2181 RANDOM 14.887
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] -0.14 0.21 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.31 r_dihedral_angle_3_deg 14.122 r_dihedral_angle_4_deg 12.013 r_dihedral_angle_1_deg 6.848 r_angle_refined_deg 1.78 r_angle_other_deg 0.76 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.31 r_dihedral_angle_3_deg 14.122 r_dihedral_angle_4_deg 12.013 r_dihedral_angle_1_deg 6.848 r_angle_refined_deg 1.78 r_angle_other_deg 0.76 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1036 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 26
Software Software Software Name Purpose SAINT data reduction APEX data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing