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Crystal structure of phenylalanine tRNA from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YCO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277.15 12.4% PEG8000, 0.2M AcCa, 0.1M Hepes pH 7, 0.1M L-Pro
Crystal Properties Matthews coefficient Solvent content 4.95 75.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.618 α = 90 b = 109.618 β = 90 c = 138.518 γ = 120
Symmetry Space Group P 64 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 278 PIXEL DECTRIS PILATUS 6M 2016-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.97857 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.1 50 99.7 0.99 14.2 12.5 9432
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 3.1 3.3 98.9 0.68
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4YCO 3.1 42.98 1.34 9420 470 99.76 0.2163 0.2153 0.2361 0.257
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.7444 f_angle_d 0.8543 f_chiral_restr 0.0391 f_plane_restr 0.0055 f_bond_d 0.0035
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1609 Solvent Atoms 2 Heterogen Atoms 29
Software Software Software Name Purpose XDS data reduction PHENIX refinement XDS data reduction XDS data scaling PHASER phasing