☰ Navigation Tabs
Crystal structure of NucA from Streptococcus agalactiae with magnesium ion bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QGO pdb entry 4QGO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 50mM Tris, 1.6M, ammonium sulfate, 10mM MgCl2 and 1:136 molar ratio of protein to 8mer duplex of 5'-GCGATCGC-3' DNA (not visible in structure), VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.44 64.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.721 α = 90 b = 123.721 β = 90 c = 157.403 γ = 120
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 RIGAKU SATURN 92 VariMaxHF 2014-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 97.2 0.08 23.7 4.4 89816 89816 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 79.9 0.33 2.8 1.7 7329
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 pdb entry 4QGO 2 24.854 1.33 89816 89709 1976 97.11 0.1575 0.155 0.1503 0.1903 0.1883 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.553 f_angle_d 0.816 f_chiral_restr 0.049 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6839 Nucleic Acid Atoms Solvent Atoms 770 Heterogen Atoms 133
Software Software Software Name Purpose StructureStudio data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling