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X-ray structure of Roquin ROQ domain in complex with a Selex-derived hexa-loop RNA motif
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QI0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 PEG 3350, NaCl, Bis-TRIS
Crystal Properties Matthews coefficient Solvent content 2.11 41.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.9 α = 90 b = 89.3 β = 90 c = 144.7 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 2M 2015-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00003 SLS X06DA
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 3 50 99.9 0.148 16.7 13.2 18598
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 3 3.08 99.9 0.938 3.1 12.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4QI0 3 50 18598 952 99.94 0.18572 0.18321 0.2338 0.208 RANDOM 66.89
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] 6.47 -2.72 -3.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.141 r_dihedral_angle_3_deg 18.959 r_dihedral_angle_4_deg 17.892 r_long_range_B_refined 7.136 r_long_range_B_other 7.135 r_dihedral_angle_1_deg 6.384 r_scangle_other 4.666 r_mcangle_it 4.167 r_mcangle_other 4.167 r_scbond_it 2.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.141 r_dihedral_angle_3_deg 18.959 r_dihedral_angle_4_deg 17.892 r_long_range_B_refined 7.136 r_long_range_B_other 7.135 r_dihedral_angle_1_deg 6.384 r_scangle_other 4.666 r_mcangle_it 4.167 r_mcangle_other 4.167 r_scbond_it 2.892 r_scbond_other 2.892 r_mcbond_it 2.57 r_mcbond_other 2.57 r_angle_other_deg 1.87 r_angle_refined_deg 1.757 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_bond_other_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.009 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4817 Nucleic Acid Atoms 1708 Solvent Atoms 49 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing