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Structural insights into cis element recognition of non- polyadenylated RNAs by the Nab3-RRM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WF2 PDB ENTRY 1WF2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 100MM SODIUM CACODYLATE BUFFER PH 6.5, 200MM SODIUM ACETATE, PEG 8000 AT 20-30 % (W/V).
Crystal Properties Matthews coefficient Solvent content 1.75 29.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.95 α = 90 b = 42.07 β = 90 c = 55.67 γ = 90
Symmetry Space Group P 21 21 21
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 2010-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 1.3 50 98.3 0.06 19.8 6 15337
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 1.3 1.4 95 0.21 7.54 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1WF2 1.3 33.56 15337 808 100 0.17567 0.17466 0.1819 0.19448 0.198 RANDOM 12.788
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] 0.22 -0.24 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.703 r_dihedral_angle_4_deg 13.807 r_dihedral_angle_3_deg 10.911 r_dihedral_angle_1_deg 6.046 r_scangle_it 3.421 r_scbond_it 2.166 r_mcangle_it 1.534 r_angle_refined_deg 1.335 r_mcbond_it 0.854 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.703 r_dihedral_angle_4_deg 13.807 r_dihedral_angle_3_deg 10.911 r_dihedral_angle_1_deg 6.046 r_scangle_it 3.421 r_scbond_it 2.166 r_mcangle_it 1.534 r_angle_refined_deg 1.335 r_mcbond_it 0.854 r_chiral_restr 0.102 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_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_other r_mcangle_other r_scbond_other 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 631 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing