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Crystal structure of human tRNA-dihydrouridine(20) synthase dsRBD in complex with a 22 nucleotide dsRNA
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 6 292 15% v/v isopropanol
20 mM MgCl2
50 mM MES
Crystal Properties Matthews coefficient Solvent content 2.72 54.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.44 α = 90 b = 115.56 β = 90 c = 66.62 γ = 90
Symmetry Space Group C 2 2 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 CCD ADSC QUANTUM 315r 2015-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98010 SOLEIL PROXIMA 2
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 3.2 43.65 97.52 0.3064 0.995 5.11 5.8 3855 100.05
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.314 93.44 0.302 0.85 3.8
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 3.2 43.65 3855 380 97.7 0.228 0.226 0.2613 0.242 0.2752 RANDOM 99.32
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] 11.5331 -8.5683 -2.9649
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.85 t_omega_torsion 2.4 t_angle_deg 0.85 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.85 t_omega_torsion 2.4 t_angle_deg 0.85 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 718 Nucleic Acid Atoms 468 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing