☰ Navigation Tabs
Crystal structure of Staphylococcal nuclease variant Delta+PHS L36K L103K 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 20% MPD, 25 mM potassium phosphate, calcium chloride, pdTp
Crystal Properties Matthews coefficient Solvent content 2.32 46.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.195 α = 90 b = 78.933 β = 90.18 c = 60.891 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 AGILENT ATLAS CCD 2016-01-29 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 1.95 60.89 99.9 0.047 28.05 9.7 21550 22.8
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 1.95 2.02 99.9 0.216 4.46 6.1
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 1.95 60.89 20492 1040 99.94 0.2015 0.1996 0.2062 0.2378 0.2456 RANDOM 16.195
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] 0.01 0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.509 r_dihedral_angle_3_deg 16.297 r_dihedral_angle_4_deg 9.373 r_dihedral_angle_1_deg 6.381 r_mcangle_it 2.061 r_angle_refined_deg 1.806 r_mcbond_it 1.308 r_mcbond_other 1.303 r_angle_other_deg 0.941 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.509 r_dihedral_angle_3_deg 16.297 r_dihedral_angle_4_deg 9.373 r_dihedral_angle_1_deg 6.381 r_mcangle_it 2.061 r_angle_refined_deg 1.806 r_mcbond_it 1.308 r_mcbond_other 1.303 r_angle_other_deg 0.941 r_chiral_restr 0.102 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2070 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XPREP data reduction PHASER phasing PDB_EXTRACT data extraction CrysalisPro data reduction