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Crystal structure of guanine riboswitch bound to 2-aminopurine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U8D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20% PEG 3K, 12.5 mM cobalt hexammine, 600mM ammonium acetate, 10 mM K-HEPES., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.2 44.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.43 α = 90 b = 35.16 β = 91.18 c = 42.24 γ = 90
Symmetry Space Group C 1 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 IMAGE PLATE RIGAKU RAXIS IV 2008-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.4 19.92 94.2 0.08 8.1 1.83 13481 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.49 86 0.284 3 1.64
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 1U8D 2.4 19.92 13374 1296 93.4 0.229 0.229 0.2228 0.278 0.2712 RANDOM 40.1
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] 6.97 8.8 -11.53 4.57
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.6 c_improper_angle_d 1.2 c_angle_deg 0.6 c_bond_d 0.003 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.6 c_improper_angle_d 1.2 c_angle_deg 0.6 c_bond_d 0.003 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1422 Solvent Atoms 64 Heterogen Atoms 91
Software Software Software Name Purpose CrystalClear data collection CNS refinement d*TREK data reduction d*TREK data scaling CNS phasing