☰ Navigation Tabs
Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 293 PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.98 58.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.281 α = 90 b = 83.062 β = 90 c = 233.573 γ = 90
Symmetry Space Group I 2 2 2
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 2014-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.979 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.2 50 99.2 0.166 0.165 0.056 5.1 12.2 9964 86.47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.26 91.1 0.491 0.513 6.8 438
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FREE R-VALUE 3.209 48.787 1.33 8069 1807 98.18 0.2553 0.2517 0.2556 0.2892 0.2915 Random selection 100.4238
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 14.753 f_angle_d 0.728 f_chiral_restr 0.027 f_bond_d 0.003 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 658 Nucleic Acid Atoms 2033 Solvent Atoms Heterogen Atoms 98
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling PDB_EXTRACT data extraction