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The crystal structure of YegTK267A from the Nucleoside: H+ Symporter Family
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DL9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 0.1 M MES (pH=5.8), 0.1 M Li2SO4, 0.1 M glycine, and 26% PEG550MME
Crystal Properties Matthews coefficient Solvent content 2.5 50.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.769 α = 77.85 b = 58.212 β = 81.3 c = 105.076 γ = 68.46
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 PILATUS 6M 2019-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL18U 0.9793 NFPSS BL18U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.91 50 98.1 0.078 0.111 0.996 4.03 3.43 20090
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 2.91 3.09 1.594 0.929 0.127
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.913 39.139 1.96 19644 1967 97.96 0.2434 0.2413 0.2439 0.2619 0.2651
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 22.948 f_angle_d 1.378 f_chiral_restr 0.068 f_bond_d 0.011 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6199 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 165
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing