☰ Navigation Tabs
Crystal structure of SepRS-SepCysE from Methanocaldococcus jannaschii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7 293 0.1M Tris-HCl pH7.0, 0.3M Ammonium sulfate, 36% MPD
Crystal Properties Matthews coefficient Solvent content 5.12 82.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 279.821 α = 90 b = 279.821 β = 90 c = 279.821 γ = 90
Symmetry Space Group I 21 3
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 ADSC QUANTUM 315r 2015-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 3.1 48 99.9 0.13 16.2 7.6 65670
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2DU7 3.101 47.989 1.35 65625 3328 99.85 0.186 0.1847 0.1942 0.2092 0.2163
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 16.26 f_angle_d 1.346 f_chiral_restr 0.063 f_bond_d 0.014 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9182 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 72
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing