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Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, manganese Soak
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.05 M Na-HEPES, pH 7.5, ~40 % (v/v) pentaerythritol propoxylate, 0.2 M KCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 43.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.031 α = 90 b = 34.632 β = 92.81 c = 111.598 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 CCD ADSC QUANTUM 315 2010-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.5 NSLS X29A
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 97.9 0.136 19.9 5.9 7069 6921
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 3.21 85.2 0.24 6.6 4.5 586
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 Molrep THROUGHOUT 3.1 20 6532 317 98.12 0.19867 0.19607 0.2043 0.252 0.2558 RANDOM 64.159
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] -4.68 -7.95 -3.66 7.57
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.186 r_angle_refined_deg 1.132 r_scbond_it 0.702 r_nbtor_refined 0.283 r_nbd_refined 0.186 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.171 r_symmetry_vdw_refined 0.141 r_chiral_restr 0.057 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.186 r_angle_refined_deg 1.132 r_scbond_it 0.702 r_nbtor_refined 0.283 r_nbd_refined 0.186 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.171 r_symmetry_vdw_refined 0.141 r_chiral_restr 0.057 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_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it 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 2826 Solvent Atoms 10 Heterogen Atoms 57
Software Software Software Name Purpose CBASS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling