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Crystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in a closed state bound to laminaritriose (Form I)
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, 40% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.21 44.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.93 α = 90 b = 63.55 β = 90 c = 110.23 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 IMAGE PLATE RIGAKU RAXIS IV++ VariMax HF 2019-09-18 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 2.3 57.93 99.8 0.105 0.112 0.037 0.996 16.1 8.8 18713
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 2.3 2.38 99.3 0.356 0.377 0.123 0.961 8.5
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 2.3 55.06 17774 867 99.63 0.2054 0.2026 0.2076 0.2649 0.2717 RANDOM 24.888
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] 6.23 7.72 -13.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.63 r_dihedral_angle_4_deg 19.812 r_dihedral_angle_3_deg 17.997 r_dihedral_angle_1_deg 7.311 r_angle_refined_deg 1.931 r_angle_other_deg 1.46 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.63 r_dihedral_angle_4_deg 19.812 r_dihedral_angle_3_deg 17.997 r_dihedral_angle_1_deg 7.311 r_angle_refined_deg 1.931 r_angle_other_deg 1.46 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3156 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 54
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