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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 6SLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.5 293 15% PEG1000
0.05 M Li-sulphate
0.05 M Na-phosphate monobasic
0.08 M Na-citrate
Crystal Properties Matthews coefficient Solvent content 3.71 66.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.781 α = 90 b = 142.734 β = 90 c = 250.048 γ = 90
Symmetry Space Group P 21 21 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 2019-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.917 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 2.61 142.7 99.9 0.278 0.102 0.995 5.6 7.3 141223 43.15
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 2.61 2.65 2.079 0.752 0.53 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 6SLI 2.61 123.96 1.33 140898 6888 99.67 0.2096 0.2067 0.2082 0.2642 0.264 54.61
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 6.4561 f_angle_d 1.0246 f_chiral_restr 0.0534 f_bond_d 0.0079 f_plane_restr 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21974 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 277
Software Software Software Name Purpose PHENIX refinement PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing