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Crystal structure of the triple-helical stability element at the 3' end of MALAT1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Folded RNA was combined with an equal volume of the reservoir solution (50 mM sodium cacodylate pH 6.5, 18 mM magnesium chloride, 2.5 mM spermine and 9% isopropanol)
Crystal Properties Matthews coefficient Solvent content 3.56 65.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.82 α = 90 b = 162.82 β = 90 c = 65.93 γ = 120
Symmetry Space Group P 32 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 PIXEL DECTRIS PILATUS 6M 2012-12-15 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-02-16 M MAD 3 1 100
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C 2 SYNCHROTRON NSLS BEAMLINE X25 1.1053, 1.1060, 1.1046 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 99.7 17.2 11.2 17565
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.18 99.8 1.28 11.3
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 THROUGHOUT 3.1 48.2 17565 915 99.7 0.222 0.22 0.224 0.255 0.2578 RANDOM 51.04
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] 0.68 0.68 0.68 -2.2
RMS Deviations Key Refinement Restraint Deviation r_angle_other_deg 1.462 r_angle_refined_deg 1.026 r_chiral_restr 0.142 r_gen_planes_refined 0.012 r_bond_refined_d 0.01 r_gen_planes_other 0.008 r_bond_other_d 0.007 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg
RMS Deviations Key Refinement Restraint Deviation r_angle_other_deg 1.462 r_angle_refined_deg 1.026 r_chiral_restr 0.142 r_gen_planes_refined 0.012 r_bond_refined_d 0.01 r_gen_planes_other 0.008 r_bond_other_d 0.007 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined 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 4709 Solvent Atoms 35 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction