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Crystal structure of Staphylococcal nuclease variant Delta+PHS A109R at cryogenic temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TQO PDB entry 1tqo, all waters removed, b = 20.0, ILE-92 truncated to ALA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 43% MPD, 25 mM Potassium Phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.31 46.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.09 α = 90 b = 59.843 β = 90 c = 73.558 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 100 CCD BRUKER APEX II multi-layer optics 2006-11-10 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 1.9 34.1 99.7 0.0196 0.0394 41.54 12.05 12416 12416 23.7
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) 1 1.9 2 98.4 0.1077 0.188 8.46 5.91 1692
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-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1tqo, all waters removed, b = 20.0, ILE-92 truncated to ALA 1.9 31.3 12441 12337 1215 99.16 0.197 0.197 0.191 0.196 0.252 RANDOM 16.382
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 0.03 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.123 r_dihedral_angle_3_deg 13.174 r_dihedral_angle_4_deg 8.413 r_sphericity_free 6.102 r_dihedral_angle_1_deg 6.083 r_scangle_it 3.836 r_sphericity_bonded 2.895 r_scbond_it 2.639 r_mcangle_it 1.98 r_rigid_bond_restr 1.734
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.123 r_dihedral_angle_3_deg 13.174 r_dihedral_angle_4_deg 8.413 r_sphericity_free 6.102 r_dihedral_angle_1_deg 6.083 r_scangle_it 3.836 r_sphericity_bonded 2.895 r_scbond_it 2.639 r_mcangle_it 1.98 r_rigid_bond_restr 1.734 r_angle_refined_deg 1.43 r_mcbond_it 1.308 r_nbtor_refined 0.302 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.151 r_symmetry_hbond_refined 0.144 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.12 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1065 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 13
Software Software Software Name Purpose SAINT data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction APEX data collection SAINT data reduction