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Crystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in an open-liganded state bound to gentiobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7C63
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 293 0.2 M Ammonium sulphate, 45% PEG 8000
Crystal Properties Matthews coefficient Solvent content 1.99 38.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.34 α = 90 b = 91.54 β = 112.51 c = 69.39 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE RIGAKU RAXIS IV++ VariMax HF 2019-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.9 48.75 94.5 0.085 0.096 0.043 0.995 10.6 4.7 53435
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 1.9 1.94 89.3 0.431 0.485 0.219 0.891 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7C63 1.9 48.75 50810 2572 94.07 0.1761 0.1735 0.1814 0.2273 0.2338 RANDOM 27.588
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] -6.98 -2.2 3.23 3.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.687 r_dihedral_angle_4_deg 19.094 r_dihedral_angle_3_deg 15.448 r_dihedral_angle_1_deg 6.923 r_angle_refined_deg 1.92 r_angle_other_deg 1.477 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.687 r_dihedral_angle_4_deg 19.094 r_dihedral_angle_3_deg 15.448 r_dihedral_angle_1_deg 6.923 r_angle_refined_deg 1.92 r_angle_other_deg 1.477 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6396 Nucleic Acid Atoms Solvent Atoms 470 Heterogen Atoms 80
Software Software Software Name Purpose HKL-3000 data collection MOSFLM data reduction Aimless data scaling PHASER phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction