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Crystal structure of the glycine riboswitch bound to glycine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OWI PDB ENTRY 3OWI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.1 293.15 0.05 M Na-cacodylate, pH 5.1, 0.2 M KCl, 8 % (w/v) PEG8000 and 80 mM magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 3.48 64.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.514 α = 90 b = 83.514 β = 90 c = 198.524 γ = 120
Symmetry Space Group P 32 2 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 CCD ADSC QUANTUM 315 2010-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0750 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 20 99.3 20410 20267 -3 -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) 2.8 2.9 99.4 0.45 4.1 6.1 1995
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 3OWI 2.802 20 18284 18182 2065 99.44 0.20794 0.20794 0.2048 0.2157 0.23641 0.2443 RANDOM 69.125
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 r_angle_refined_deg 1.003 r_scangle_it 0.942 r_scbond_it 0.544 r_mcangle_it 0.128 r_mcbond_it 0.081 r_chiral_restr 0.045 r_bond_refined_d 0.005 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 3785 Solvent Atoms 102 Heterogen Atoms 43
Software Software Software Name Purpose CBASS data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing