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Crystal structure of the dsRBD domain of tRNA-dihydrouridine(20) synthase from Amphimedon queenslandica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WFT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 0.1 M Hepes pH 7.5, 1.4 M tri-sodium citrate, 15 mg/ml protein in 50 mM Tris, pH 8 300 mM NaCl 5mM mercaptoethanol
Crystal Properties Matthews coefficient Solvent content 2.01 38.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.077 α = 90 b = 56.895 β = 93.05 c = 63.587 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 9M 2018-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98011 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.676 42.373 97.9 0.074 0.09 0.051 0.997 7.8 2.9 23361
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.676 1.705 79.7 0.975 1.245 0.762 0.351 0.8 2
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 4wft 1.676 29.04 23356 1170 97.8 0.2047 0.2035 0.1963 0.2278 0.2219 RANDOM 28.45
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] -1.9139 -1.3752 -1.5478 3.4616
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 12.48 t_omega_torsion 3.6 t_angle_deg 1.02 t_bond_d 0.009 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1548 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 28
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction XDS data scaling PHASER phasing