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Crystal structure of Staphylococcal nuclease variant Delta+PHS Y91D 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 26% MPD, 25 mM potassium phosphate, calcium chloride, pdTp
Crystal Properties Matthews coefficient Solvent content 2.24 45.14
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 2016-03-17 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 1.895 50 100 0.02 48.99 9.3 11143 30.14
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 1.895 1.97 100 0.128 5.93 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 1.895 38.35 10534 594 97.79 0.1939 0.1912 0.2018 0.2448 0.2526 RANDOM 28.052
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] -1.48 0.1 -0.06 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.766 r_dihedral_angle_3_deg 19.907 r_dihedral_angle_4_deg 17.594 r_dihedral_angle_1_deg 7.206 r_mcangle_it 2.014 r_angle_refined_deg 1.938 r_mcbond_it 1.406 r_mcbond_other 1.383 r_angle_other_deg 0.892 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.766 r_dihedral_angle_3_deg 19.907 r_dihedral_angle_4_deg 17.594 r_dihedral_angle_1_deg 7.206 r_mcangle_it 2.014 r_angle_refined_deg 1.938 r_mcbond_it 1.406 r_mcbond_other 1.383 r_angle_other_deg 0.892 r_chiral_restr 0.121 r_bond_refined_d 0.018 r_gen_planes_refined 0.016 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1029 Nucleic Acid Atoms Solvent Atoms 72 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