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X-ray structure of Roquin ROQ domain in complex with a UCP3 CDE1 SL RNA motif
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QI2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 0.01 M Bis Tris Propane pH 6.5, 0.29 M Sodium Tartrate, 19 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.6 52.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.99 α = 90 b = 86.99 β = 90 c = 72.99 γ = 90
Symmetry Space Group P 42 21 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 2M-F 2019-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 96.9 0.047 1 23.16 8.4 36355 31
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.64 75.5 0.736 0.797 2.46 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 4QI2 1.6 47.08 34595 1760 96.85 0.1582 0.1563 0.1686 0.1972 0.2049 RANDOM 28.248
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] -0.14 -0.14 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.524 r_dihedral_angle_4_deg 17.292 r_dihedral_angle_3_deg 11.965 r_dihedral_angle_1_deg 5.608 r_angle_refined_deg 1.836 r_angle_other_deg 1.597 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.524 r_dihedral_angle_4_deg 17.292 r_dihedral_angle_3_deg 11.965 r_dihedral_angle_1_deg 5.608 r_angle_refined_deg 1.836 r_angle_other_deg 1.597 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1225 Nucleic Acid Atoms 400 Solvent Atoms 255 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing