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Crystal structure of sugar-bound melibiose permease MelB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 297.15 50 mM BaCl2, 50 mM CaCl2, 100 mM Tris-HCl, pH 8.5, and 29-32% PEG 400, 6 mM a-NPG
Crystal Properties Matthews coefficient Solvent content 4.76 74.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.364 α = 90 b = 126.364 β = 90 c = 104.334 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 PILATUS3 6M 2018-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.97949 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) 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 29.8945 99.6949 0.109 0.114 0.034 20.5 21 18680 98.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.05 3.26 99.9 1.37 1.43 0.419 0.3 2.4 22.5
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 SAD FREE R-VALUE 3.05 29.89 1.33 18617 1856 99.65 0.2627 0.2594 0.2658 0.2935 0.2962 107.02
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 4.096 f_angle_d 0.536 f_chiral_restr 0.0363 f_plane_restr 0.0035 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3561 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling CRANK2 phasing