☰ Navigation Tabs
Structure of unmodified E. coli tRNA(Asp)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EHZ PDB entry 1EHZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 287 2 uL 20 mg/ml E. coli tRNA(Asp) + 2 uL equilibration solution (50 mM sodium cacodylate, pH 7.5, 30% MPD, 10 mM spermine tetrahydrochloride, 300 mM sodium chloride, 300 mM potassium chloride) + 0.5 uL 0.25% w/v p-coumaric acid, 0.25% w/v phenylurea, 0.25% w/v poly(3-hydroxybutyric acid), 0.25% w/v sulfaguanidine, 0.02 M sodium HEPES, pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.38 48.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.677 α = 90 b = 64.677 β = 90 c = 195.799 γ = 120
Symmetry Space Group P 31 2 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 Monochromator 2017-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0782 APS 21-ID-D
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 1.95 48.62 94 0.155 0.158 0.029 0.992 15.8 30 35638
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 1.95 2.056 50.8 2.683 2.724 0.468 0.488 1.8 33.7
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 PDB entry 1EHZ 1.95 48.62 30070 1469 88.5 0.2164 0.2154 0.2214 0.2381 0.2446 RANDOM 50.999
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] 2.3 2.3 -4.59
RMS Deviations Key Refinement Restraint Deviation r_angle_other_deg 1.298 r_angle_refined_deg 0.85 r_chiral_restr 0.07 r_gen_planes_refined 0.005 r_bond_refined_d 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 3288 Solvent Atoms 23 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction STARANISO data scaling PHASER phasing