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Crystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in a closed state bound to laminaritriose (Form II)
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 2.68 54.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.41 α = 90 b = 185.41 β = 90 c = 74.18 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 IMAGE PLATE RIGAKU RAXIS IV++ VariMax HF 2019-09-17 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 2.8 80.28 100 0.108 0.113 0.034 0.999 19.1 11.1 34597
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 2.8 3.06 100 0.438 0.461 0.144 0.954 10.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7C63 2.8 80.28 34597 1703 99.93 0.1889 0.1866 0.2356 0.2329 RANDOM 55.799
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] 5.11 5.11 -10.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.888 r_dihedral_angle_3_deg 21.02 r_dihedral_angle_4_deg 20.244 r_dihedral_angle_1_deg 6.907 r_angle_refined_deg 1.841 r_angle_other_deg 1.374 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.888 r_dihedral_angle_3_deg 21.02 r_dihedral_angle_4_deg 20.244 r_dihedral_angle_1_deg 6.907 r_angle_refined_deg 1.841 r_angle_other_deg 1.374 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9455 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 153
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