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Crystallization of the Thermotoga maritima lysine riboswitch in free form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DIL pdb entry 3DIL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.7 293 18% PEG 4000, 0.1M Sodium Citrate, 20% isopropanol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.67 53.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.252 α = 90 b = 78.624 β = 90 c = 141.876 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS 2008-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 20 92.8 0.197 7.5 4.3 11469 10643
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 3.1 3.2 89.5 0.499 2.8 4.3 1124
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3DIL 3.1 20 10917 10098 516 92.5 0.1896 0.1896 0.18773 0.1961 0.22764 0.2325 RANDOM 39.715
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] -2.94 -3.8 6.74
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.228 r_scangle_it 0.819 r_scbond_it 0.472 r_nbtor_refined 0.27 r_symmetry_hbond_refined 0.184 r_symmetry_vdw_refined 0.164 r_nbd_refined 0.158 r_xyhbond_nbd_refined 0.146 r_mcbond_it 0.099 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.228 r_scangle_it 0.819 r_scbond_it 0.472 r_nbtor_refined 0.27 r_symmetry_hbond_refined 0.184 r_symmetry_vdw_refined 0.164 r_nbd_refined 0.158 r_xyhbond_nbd_refined 0.146 r_mcbond_it 0.099 r_chiral_restr 0.068 r_metal_ion_refined 0.04 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 3752 Solvent Atoms 6 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing