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Crystallization of the Thermotoga maritima lysine riboswitch bound to L-4-oxalysine
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 2.71 54.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.541 α = 90 b = 79.095 β = 90 c = 142.535 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 CCD ADSC QUANTUM 4 2008-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.24 APS 24-ID-C
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 2.5 20 97.7 0.085 27.8 6 22228 21717
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 2.5 2.59 95.2 0.497 4.3 5.9 2170
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 refmac THROUGHOUT pdb entry 3DIL 2.5 20 20868 20432 1095 97.91 0.21423 0.21423 0.21151 0.2116 0.26788 0.2663 RANDOM 32.023
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] -1.57 -4.24 5.81
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.254 r_scangle_it 0.946 r_scbond_it 0.638 r_mcangle_it 0.276 r_nbtor_refined 0.265 r_mcbond_it 0.262 r_nbd_refined 0.163 r_metal_ion_refined 0.153 r_symmetry_vdw_refined 0.153 r_symmetry_hbond_refined 0.151
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.254 r_scangle_it 0.946 r_scbond_it 0.638 r_mcangle_it 0.276 r_nbtor_refined 0.265 r_mcbond_it 0.262 r_nbd_refined 0.163 r_metal_ion_refined 0.153 r_symmetry_vdw_refined 0.153 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_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 3752 Solvent Atoms 83 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement CBASS data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing