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E. coli dihydrouridine synthase C (DusC) in complex with tRNATrp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BFA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M Bis-Tris pH 6.5, 0.2 M Li2SO4 26% PEG 2K MME
Crystal Properties Matthews coefficient Solvent content 2.69 54.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.516 α = 90 b = 98.516 β = 90 c = 231.172 γ = 120
Symmetry Space Group P 65 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 PSI PILATUS 6M 2014-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96861 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.55 49.26 99.6 0.141 8.8 5.3 22329 -3 44.936
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.66 99.9 1.099 1.5 5.5
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 4bfa 2.55 49.26 21202 1127 99.27 0.2095 0.2081 0.2139 0.235 0.2357 RANDOM 49.616
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] -0.52 -0.26 -0.52 1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.222 r_dihedral_angle_4_deg 16.998 r_dihedral_angle_3_deg 12.994 r_dihedral_angle_1_deg 5.578 r_angle_other_deg 1.044 r_angle_refined_deg 1.003 r_mcangle_it 0.562 r_mcbond_it 0.318 r_mcbond_other 0.318 r_chiral_restr 0.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.222 r_dihedral_angle_4_deg 16.998 r_dihedral_angle_3_deg 12.994 r_dihedral_angle_1_deg 5.578 r_angle_other_deg 1.044 r_angle_refined_deg 1.003 r_mcangle_it 0.562 r_mcbond_it 0.318 r_mcbond_other 0.318 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2398 Nucleic Acid Atoms 1287 Solvent Atoms 52 Heterogen Atoms 42
Software Software Software Name Purpose XDS data reduction XDS data scaling Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction