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Crystal structure of Staphylococcal nuclease variant Delta+PHS V23T/V66T at cryogenic temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BDC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 20% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 8.0, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.23 44.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.153 α = 90 b = 60.402 β = 94.48 c = 38.472 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 100 CCD APEX II CCD Multilayer 2013-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54
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 1.66 50 100 0.015 6.56 20.39 16877 16877 25.4
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 1.66 1.76 100 0.1175 6.56 5.83 2701
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 3BDC 1.66 38.35 15965 15965 848 99.71 0.189 0.189 0.1867 0.1902 0.2322 0.2352 RANDOM 19.225
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] -0.83 0.49 -1.21 2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.788 r_dihedral_angle_3_deg 16.46 r_dihedral_angle_4_deg 7.15 r_dihedral_angle_1_deg 6.582 r_angle_refined_deg 1.975 r_chiral_restr 0.158 r_bond_refined_d 0.019 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1033 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 26
Software Software Software Name Purpose DENZO data reduction XPREP data reduction PHASER phasing REFMAC refinement PDB_EXTRACT data extraction APEX data collection APEX data reduction