☰ Navigation Tabs
SAM-I riboswitch containing the T. solenopsae Kt-23 in complex with S- adenosyl methionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GX5 PDB ENTRY 3GX5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 40 MM NA-CACODYLATE PH 7, 80 MM KCL, 30 MM BACL2, 12 MM SPERMINE HCL 8%(V/V) MPD
Crystal Properties Matthews coefficient Solvent content 2.42 65.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.3 α = 90 b = 61.3 β = 90 c = 157.538 γ = 90
Symmetry Space Group P 43 21 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 CCD 2011-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.95 50 98.5 0.11 26.8 9.5 6810 3
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 2.95 3.06 89.5 0.46 3.05 8.2
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 3GX5 2.95 50 6386 313 97.74 0.1914 0.18906 0.1748 0.23943 0.2169 RANDOM 74.637
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] 46.09 46.09 -92.19
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 2.545 r_chiral_restr 0.133 r_gen_planes_refined 0.023 r_bond_refined_d 0.016 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 2.545 r_chiral_restr 0.133 r_gen_planes_refined 0.023 r_bond_refined_d 0.016 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other 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 2024 Solvent Atoms 10 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALA data scaling MOLREP phasing