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Crystal structure of Staphylococcal nuclease variant Delta+PHS Y91E 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 25% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 8.0, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.36 47.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.022 α = 90 b = 81.293 β = 90.05 c = 60.385 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 BRUKER APEX II multi-layer optics 2008-02-06 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) R Sym 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 2 60.38 99.9 0.0635 0.0226 38.84 11.3 17596 17583 20.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.1 0.0996 0.0594 15.41 4.85 2296
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3BDC 2.1 60.38 17570 17554 1781 99.91 0.2423 0.239 0.233 0.29 0.2015 RANDOM 8.908
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 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.225 r_dihedral_angle_3_deg 16.847 r_dihedral_angle_4_deg 11.916 r_dihedral_angle_1_deg 6.15 r_scangle_it 1.837 r_angle_refined_deg 1.316 r_scbond_it 1.198 r_mcangle_it 0.788 r_mcbond_it 0.545 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.225 r_dihedral_angle_3_deg 16.847 r_dihedral_angle_4_deg 11.916 r_dihedral_angle_1_deg 6.15 r_scangle_it 1.837 r_angle_refined_deg 1.316 r_scbond_it 1.198 r_mcangle_it 0.788 r_mcbond_it 0.545 r_nbtor_refined 0.298 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.147 r_chiral_restr 0.083 r_metal_ion_refined 0.044 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2060 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 52
Software Software Software Name Purpose SAINT data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction APEX data collection SAINT data reduction