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Crystal structure of thiamine pyrophosphate-specific riboswitch in complex with thiamine pyrophosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.9 293 28 % PEG4000, 100 mM Na-acetate, pH 4.8, and 200 mM NH4-acetate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.90
Crystal Properties Matthews coefficient Solvent content 2 38.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.819 α = 90 b = 29.558 β = 94.55 c = 95.17 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 2005-11-07 M SINGLE WAVELENGTH 2 1 x-ray CCD ADSC QUANTUM 315 2005-11-07 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 NSLS X25 2 SYNCHROTRON NSLS BEAMLINE X25 1.1407, 1.1411, 1.1201 NSLS X25
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 2.05 20 99.8 0.062 4.3 27007
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 2.05 2.12 100 0.475 2.89 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 MAD THROUGHOUT 2.05 20 25309 25258 1337 99.8 0.21 0.208 0.2089 0.241 0.2441 RANDOM 34.95
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] -0.76 -2.37 1.81 -1.43
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.196 r_angle_refined_deg 1.043 r_scbond_it 0.85 r_mcangle_it 0.435 r_nbtor_refined 0.284 r_mcbond_it 0.199 r_xyhbond_nbd_refined 0.191 r_symmetry_hbond_refined 0.177 r_nbd_refined 0.164 r_symmetry_vdw_refined 0.16
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 1.196 r_angle_refined_deg 1.043 r_scbond_it 0.85 r_mcangle_it 0.435 r_nbtor_refined 0.284 r_mcbond_it 0.199 r_xyhbond_nbd_refined 0.191 r_symmetry_hbond_refined 0.177 r_nbd_refined 0.164 r_symmetry_vdw_refined 0.16 r_metal_ion_refined 0.141 r_chiral_restr 0.129 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 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 3442 Solvent Atoms 312 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement CAD4 data reduction HKL-2000 data scaling SOLVE phasing