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Structure of the RagAB peptide transporter
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CX8 5CX8, 5FQ8 experimental model PDB 5FQ8 5CX8, 5FQ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 18% PEG200
0.1 M KCl
0.1 M K-phosphate
Crystal Properties Matthews coefficient Solvent content 5.33 76.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 190.56 α = 90 b = 376.87 β = 90 c = 369.24 γ = 90
Symmetry Space Group C 2 2 21
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-F 2017-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.928 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.38 83.92 99.9 0.234 0.084 0.992 8.5 7.6 184493 83.77
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.38 3.44 100 1.276 0.449 0.735 8.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5CX8, 5FQ8 3.38 83.92 1.34 184132 9218 99.74 0.2068 0.2045 0.2096 0.2511 0.2541 101.34
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 5.3979 f_angle_d 1.4546 f_chiral_restr 0.0731 f_bond_d 0.0118 f_plane_restr 0.0096
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 43884 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing