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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 2XNQ PDB ENTRY 2XNQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 85MM SODIUM ACETATE BUFFER PH 4.6, 170MM AMMONIUM ACETATE, 25.5% (W/V) PEG 4000, 15% (V/V) GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.15 48.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.64 α = 90 b = 30.64 β = 90 c = 82.42 γ = 90
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 2010-03-29 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 1.6 50 98.9 0.09 14.91 6.3 9510
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 1.6 1.7 96.3 0.43 5.26 6.3
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 2XNQ 1.6 30.64 9510 501 100 0.1615 0.16032 0.1759 0.1842 0.2003 RANDOM 19.685
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] 0.32 0.32 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.858 r_dihedral_angle_3_deg 11.191 r_dihedral_angle_4_deg 8.955 r_scangle_it 3.434 r_scbond_it 2.163 r_mcangle_it 1.385 r_angle_refined_deg 1.252 r_mcbond_it 0.695 r_chiral_restr 0.084 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.858 r_dihedral_angle_3_deg 11.191 r_dihedral_angle_4_deg 8.955 r_scangle_it 3.434 r_scbond_it 2.163 r_mcangle_it 1.385 r_angle_refined_deg 1.252 r_mcbond_it 0.695 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_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 604 Nucleic Acid Atoms 65 Solvent Atoms 47 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing