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Crystal structure of Staphylococcal nuclease variant Delta+PHS L103D 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 8 277 22% MPD, 25 mM potassium phosphate, calcium chloride, pdTp
Crystal Properties Matthews coefficient Solvent content 2.23 44.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.178 α = 90 b = 60.353 β = 93.52 c = 38.425 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 2016-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OTHER 1.5418
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 1.9 50 99.9 0.018 54.11 10.2 11215 28.19
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 1.9 1.97 99.9 0.113 7.6 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 1.9 38.35 10603 597 98.66 0.1803 0.1774 0.186 0.2349 0.2399 RANDOM 24.207
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] -1.15 -0.77 1.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.782 r_dihedral_angle_3_deg 18.1 r_dihedral_angle_4_deg 7.344 r_dihedral_angle_1_deg 6.79 r_angle_refined_deg 1.916 r_mcangle_it 1.69 r_mcbond_it 1.136 r_mcbond_other 1.115 r_angle_other_deg 0.938 r_chiral_restr 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.782 r_dihedral_angle_3_deg 18.1 r_dihedral_angle_4_deg 7.344 r_dihedral_angle_1_deg 6.79 r_angle_refined_deg 1.916 r_mcangle_it 1.69 r_mcbond_it 1.136 r_mcbond_other 1.115 r_angle_other_deg 0.938 r_chiral_restr 0.14 r_bond_refined_d 0.019 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1033 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement CrysalisPro data scaling PHASER phasing PDB_EXTRACT data extraction CrysalisPro data reduction Coot model building