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Crystal structure of beta-glycosides-binding protein (W177X) of ABC transporter in a closed state bound to cellotriose (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, 60% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.22 44.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61 α = 90 b = 100.34 β = 90 c = 133.23 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 2019-04-12 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 2.4 66.61 99.9 0.131 0.142 0.054 0.994 11.4 6.6 32723
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 2.4 2.49 99.5 0.517 0.563 0.219 0.905 6.2
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 2.4 66.61 31019 1645 99.81 0.1947 0.1911 0.1964 0.2634 0.2624 RANDOM 28.456
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] -14.98 5.72 9.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.102 r_dihedral_angle_3_deg 17.813 r_dihedral_angle_4_deg 17.382 r_dihedral_angle_1_deg 7.067 r_angle_refined_deg 1.78 r_angle_other_deg 1.414 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.102 r_dihedral_angle_3_deg 17.813 r_dihedral_angle_4_deg 17.382 r_dihedral_angle_1_deg 7.067 r_angle_refined_deg 1.78 r_angle_other_deg 1.414 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6360 Nucleic Acid Atoms Solvent Atoms 327 Heterogen Atoms 87
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