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Crystal structure of Human tRNA dihydrouridine synthase 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SeMet model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 292 0.1 M MES Malic Tris pH 4, 25% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.13 40.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.252 α = 90 b = 49.562 β = 95.71 c = 69.612 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 CCD ADSC QUANTUM 315r 2011-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.9 46.02 97.6 0.063 0.075 0.04 10.3 3 24244 24244
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 97.8 0.585 0.585 0.414 1.3 2.8 3515
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 SeMet model 1.9 46.02 22995 1236 97.17 0.1699 0.1679 0.1767 0.2065 0.2153 RANDOM 36.622
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] -0.27 0.12 1.1 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.46 r_dihedral_angle_4_deg 17.392 r_dihedral_angle_3_deg 13.263 r_dihedral_angle_1_deg 5.785 r_mcangle_it 2.118 r_angle_refined_deg 1.507 r_mcbond_it 1.446 r_mcbond_other 1.436 r_angle_other_deg 0.828 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.46 r_dihedral_angle_4_deg 17.392 r_dihedral_angle_3_deg 13.263 r_dihedral_angle_1_deg 5.785 r_mcangle_it 2.118 r_angle_refined_deg 1.507 r_mcbond_it 1.446 r_mcbond_other 1.436 r_angle_other_deg 0.828 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2466 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction XDS data reduction