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Crystal Structure of human tRNA-dihydrouridine(20) synthase catalytic domain Q305K mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XP7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 2.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.94 58.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.08 α = 90 b = 84.11 β = 90 c = 144.35 γ = 90
Symmetry Space Group I 2 2 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 EIGER X 9M 2016-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980105 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 2.25 43.61 93.4 0.137 0.998 12.6 9.2 16301
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.45 93.53 1.609 1.714 0.385 1.4 8.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4XP7 2.25 43.61 16301 799 77.2 0.183 0.181 0.1936 0.223 0.1954 RANDOM 55.39
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] 0.4593 -1.8734 1.4141
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.72 t_omega_torsion 2.83 t_angle_deg 1.13 t_bond_d 0.01 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 18.72 t_omega_torsion 2.83 t_angle_deg 1.13 t_bond_d 0.01 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 2344 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 57
Software Software Software Name Purpose BUSTER refinement XDS data reduction STARANISO data scaling PHASER phasing