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Crystal structure of Staphylococcal nuclease variant Delta+PHS L125K at cryogenic temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TQO 1TQO.PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 277 32% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 9.0, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.21 44.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.075 α = 90 b = 60.453 β = 93.102 c = 38.144 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 2008-01-10 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 38.09 99.9 0.0364 0.0215 38.45 11.09 11209 11202 27.4
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) 1.9 2 99.8 0.1709 0.1616 6.05 3.9 1602
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1TQO.PDB 1.9 27.61 11209 10635 1038 95.07 0.216 0.201 0.195 0.1959 0.253 0.2528 RANDOM 21.191
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 34.047 r_dihedral_angle_3_deg 14.633 r_dihedral_angle_4_deg 10.454 r_dihedral_angle_1_deg 5.729 r_scangle_it 3.169 r_scbond_it 2.034 r_mcangle_it 1.453 r_angle_refined_deg 1.434 r_mcbond_it 0.896 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.047 r_dihedral_angle_3_deg 14.633 r_dihedral_angle_4_deg 10.454 r_dihedral_angle_1_deg 5.729 r_scangle_it 3.169 r_scbond_it 2.034 r_mcangle_it 1.453 r_angle_refined_deg 1.434 r_mcbond_it 0.896 r_nbtor_refined 0.307 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.141 r_symmetry_hbond_refined 0.141 r_symmetry_vdw_refined 0.14 r_chiral_restr 0.101 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1059 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 26
Software Software Software Name Purpose SAINT data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction APEX data collection SAINT data reduction