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Crystal Structure of Staphylococcal nuclease variant D+PHS/V66K at pH 9 determined at 100 K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BDC 3BDC (SNase D+PHS), with residues 66 and 113-116 truncated to Ala, all waters, Ca2+ and THP removed, and all b-factors truncated to 20.00A^2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 277 39 % MPD, 25 mM Potassium phosphate, pdTp, CaCl2, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.17 43.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.051 α = 90 b = 60.439 β = 94.61 c = 37.459 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 multi-layer optics 2009-04-21 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 2 37.34 99.8 0.0283 0.0646 27.91 14.24 9409 9409 30.3
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) 2 2.1 100 0.172 0.2818 5.55 7.42 1280
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 3BDC (SNase D+PHS), with residues 66 and 113-116 truncated to Ala, all waters, Ca2+ and THP removed, and all b-factors truncated to 20.00A^2 2 37.338 9409 9408 449 99.98 0.181 0.181 0.178 0.1818 0.237 RANDOM 23.594
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 0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.564 r_dihedral_angle_3_deg 17.192 r_dihedral_angle_4_deg 11.361 r_dihedral_angle_1_deg 6.614 r_scangle_it 5.277 r_scbond_it 3.409 r_mcangle_it 2.229 r_angle_refined_deg 1.492 r_mcbond_it 1.319 r_chiral_restr 0.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.564 r_dihedral_angle_3_deg 17.192 r_dihedral_angle_4_deg 11.361 r_dihedral_angle_1_deg 6.614 r_scangle_it 5.277 r_scbond_it 3.409 r_mcangle_it 2.229 r_angle_refined_deg 1.492 r_mcbond_it 1.319 r_chiral_restr 0.144 r_bond_refined_d 0.014 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1035 Nucleic Acid Atoms Solvent Atoms 85 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