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Crystal Structure of the Twister Ribozyme with the Nucleotide 5'- to the Cleavage Site Ordered at 4.1 A Resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 160 mM sodium citrate, pH 4.6, 700 mM ammonium sulfate, 1 M lithium sulfate, 3% pentaerythriotol ethoxylate (3/4 EO/OH), 3% 6-aminohexanoic acid, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 5.31 76.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 228.77 α = 90 b = 228.77 β = 90 c = 101.06 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2014-02-21 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2014-02-21 M SINGLE WAVELENGTH 3 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2014-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.1051 APS 24-ID-C 2 SYNCHROTRON APS BEAMLINE 24-ID-C 1.8456 APS 24-ID-C 3 SYNCHROTRON APS BEAMLINE 24-ID-C 1.8445 APS 24-ID-C
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 1,2,3 2.018 198.121 99.9 0.071 19 20.6 99843 12154 2 2
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) 1,2,3 4.1 4.26 100 3.85 2 40.7
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 MIRAS THROUGHOUT 3.88 198.12 14918 14227 600 99.4 0.1873 0.18525 0.1419 0.23224 0.208 RANDOM 146.821
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] -0.85 -0.42 -0.85 2.75
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 20.016 r_scbond_it 7.2 r_angle_refined_deg 1.349 r_chiral_restr 0.113 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 20.016 r_scbond_it 7.2 r_angle_refined_deg 1.349 r_chiral_restr 0.113 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 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_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_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 4764 Solvent Atoms 6 Heterogen Atoms 4
Software Software Software Name Purpose XDS data scaling HKL2Map model building REFMAC refinement XDS data reduction HKL2Map phasing