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Crystal structure of Staphylococcal nuclease variant Delta+PHS L25D at pH 6 and 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 6 277 21% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.21 44.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.06 α = 90 b = 60.426 β = 94.16 c = 38.185 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 multi-layer optics 2013-05-13 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) 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 1.7 50 100 0.0309 19.35 11.55 15570 15570 29.8
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 1.7 1.78 100 0.2741 3.39 7.77 2422
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 PDB ENTRY 3BDC 1.7 32.22 15545 15545 778 99.95 0.1954 0.1954 0.1936 0.1929 0.227 0.2262 RANDOM 27.4532
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] -0.04 -0.01 0.03 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.758 r_dihedral_angle_3_deg 17.594 r_dihedral_angle_1_deg 7.35 r_dihedral_angle_4_deg 6.061 r_angle_refined_deg 1.996 r_chiral_restr 0.159 r_bond_refined_d 0.018 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1033 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction APEX data collection APEX data reduction PHASER phasing