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Crystal structure of the melibiose-bound melibiose transporter
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7L17
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 296.15 Tris-HCl, 100 mM, PH 8.5, NaCl, 100 mM, CaCl, 50 mM, PEG400, 34%
Crystal Properties Matthews coefficient Solvent content 4.61 73.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.421 α = 90 b = 126.421 β = 90 c = 103.555 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 PILATUS 6M 2020-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.9795 ALS 5.0.2
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 3.05 20 99.5 0.055 0.067 0.031 1 11.8 5.7 18439 122.25
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 3.05 3.26 99.5 1
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 3.05 19.7 1.34 18439 1784 99.63 0.2589 0.2551 0.2552 0.2937 0.2942 135.7
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 12.1789 f_angle_d 0.5453 f_chiral_restr 0.0377 f_plane_restr 0.0036 f_bond_d 0.0025
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3515 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 23
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing