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Crystal structure of Staphylococcal nuclease variant Delta+PHS L36E/V66H 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 9 277 25% MPD, 25 mM potassium phosphate, calcium chloride, pdTp
Crystal Properties Matthews coefficient Solvent content 2.22 44.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.116 α = 90 b = 60.283 β = 93.79 c = 38.342 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 2014-09-25 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 1.62 50 99.9 0.0169 39.7 17.62 18026 18026
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 1.62 1.64 100 0.1206 6.67 5.15
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3BDC 1.62 38.26 17010 981 99.78 0.1846 0.1826 0.2203 0.2323 RANDOM 18.015
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] -0.1 0.27 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.2 r_dihedral_angle_3_deg 13.385 r_dihedral_angle_4_deg 8.794 r_dihedral_angle_1_deg 6.754 r_angle_refined_deg 1.834 r_mcangle_it 1.775 r_mcbond_it 1.177 r_mcbond_other 1.155 r_angle_other_deg 0.831 r_chiral_restr 0.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.2 r_dihedral_angle_3_deg 13.385 r_dihedral_angle_4_deg 8.794 r_dihedral_angle_1_deg 6.754 r_angle_refined_deg 1.834 r_mcangle_it 1.775 r_mcbond_it 1.177 r_mcbond_other 1.155 r_angle_other_deg 0.831 r_chiral_restr 0.128 r_bond_refined_d 0.017 r_gen_planes_refined 0.016 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1037 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement APEX data scaling PHASER phasing PDB_EXTRACT data extraction APEX data reduction