☰ Navigation Tabs
ppGpp Riboswitch bound to ppGpp, manganese chloride structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.075 M MgCl2, 0.1 M Na-acetate pH 4.2, and 21% PEG400 (v/v)
Crystal Properties Matthews coefficient Solvent content 2.31 46.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.741 α = 90 b = 49.595 β = 97.29 c = 79.365 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 100 PIXEL DECTRIS EIGER X 16M 2018-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 1.105 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.65 30 97.4 0.107 0.049 0.876 22.5 5.3 16626
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.74 0.455 0.243
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 2.65 30 16626 850 96.9 0.21996 0.21742 0.2199 0.27218 0.2773 RANDOM 49.081
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] -4.3 0.62 3.65 0.47
RMS Deviations Key Refinement Restraint Deviation r_angle_other_deg 1.595 r_angle_refined_deg 1.223 r_chiral_restr 0.079 r_gen_planes_refined 0.007 r_bond_refined_d 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.001 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg
RMS Deviations Key Refinement Restraint Deviation r_angle_other_deg 1.595 r_angle_refined_deg 1.223 r_chiral_restr 0.079 r_gen_planes_refined 0.007 r_bond_refined_d 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.001 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 4414 Solvent Atoms 43 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing