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Crystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in a closed state bound to cellopentaose
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 44.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.23 α = 90 b = 63.23 β = 90 c = 110.08 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 2019-07-09 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 1.96 58.23 92 0.132 0.141 0.048 0.992 10.3 8.6 22403
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 1.96 2.16 94.9 0.468 0.498 0.167 0.912 8.2
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 1.96 55.04 21200 1074 74.11 0.233 0.2301 0.2339 0.2916 0.2921 RANDOM 29.642
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] -9.14 -0.06 9.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.627 r_dihedral_angle_4_deg 21.928 r_dihedral_angle_3_deg 18.918 r_dihedral_angle_1_deg 7.382 r_angle_refined_deg 1.803 r_angle_other_deg 1.352 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.627 r_dihedral_angle_4_deg 21.928 r_dihedral_angle_3_deg 18.918 r_dihedral_angle_1_deg 7.382 r_angle_refined_deg 1.803 r_angle_other_deg 1.352 r_chiral_restr 0.08 r_bond_refined_d 0.011 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 3165 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 66
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