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Crystal structure of Staphylococcal nuclease variant Delta+PHS V104E/L125E 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 7 277 22% MPD, 25 mM potassium phosphate, calcium chloride, pdTp
Crystal Properties Matthews coefficient Solvent content 2.23 44.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.065 α = 90 b = 60.36 β = 93.86 c = 38.526 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 APEX II CCD mirrors 2015-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OTHER 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 1.8 50 99.9 0.0465 16.59 5.91 13254 13254
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 1.8 1.82 100 0.2165 4.54 3.64
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 1.8 38.44 12583 652 99.91 0.1808 0.1782 0.1865 0.2324 0.2392 RANDOM 15.712
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] -0.17 0.06 -0.5 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.064 r_dihedral_angle_3_deg 18.376 r_dihedral_angle_4_deg 9.038 r_dihedral_angle_1_deg 5.728 r_angle_refined_deg 1.76 r_mcangle_it 1.206 r_angle_other_deg 0.86 r_mcbond_it 0.77 r_mcbond_other 0.742 r_chiral_restr 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.064 r_dihedral_angle_3_deg 18.376 r_dihedral_angle_4_deg 9.038 r_dihedral_angle_1_deg 5.728 r_angle_refined_deg 1.76 r_mcangle_it 1.206 r_angle_other_deg 0.86 r_mcbond_it 0.77 r_mcbond_other 0.742 r_chiral_restr 0.12 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1032 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 26
Software Software Software Name Purpose APEX data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction APEX data reduction Coot model building