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Guanine riboswitch U22C, A52G mutant bound to hypoxanthine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U8D PDB ENTRY 1U8D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 17.5% Polyethylene glycol 3000, 560mM ammonium acetate, 12.5mM cobalt hexammine chloride, 10mM K(+)-Hepes, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.23 44.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.42 α = 90 b = 35.04 β = 89.86 c = 42 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 RU-200/Confocal blue optic source 2006-06-09 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 1.95 20 97.6 0.064 10.8 3.47 14087 13749 3 26.4
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) 1.95 2.02 89.1 0.295 3.3 3.03 1219
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 1U8D 1.95 19.29 3 13741 13741 1028 97.4 0.21 0.188 0.263 0.2452 RANDOM 34.5
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] -0.29 -0.38 -3.02 3.31
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.3 c_improper_angle_d 1.93 c_angle_deg 1.4 c_bond_d 0.009 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 21.3 c_improper_angle_d 1.93 c_angle_deg 1.4 c_bond_d 0.009 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 1423 Solvent Atoms 299 Heterogen Atoms 98
Software Software Software Name Purpose CNS refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling CNS phasing