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Crystal structure of beta-glycosides-binding protein (W41A) of ABC transporter in an open state (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 VAPOR DIFFUSION, HANGING DROP 293 0.2 M Ammonium sulphate, 30% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.25 45.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.99 α = 83.39 b = 116.4 β = 88.73 c = 132.14 γ = 89.95
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 2019-04-28 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 2.65 82.19 94.1 0.264 0.309 0.16 0.793 3.5 3.5 130991
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 2.65 2.7 88.3 0.432 0.507 0.263 0.806 3.3
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 2.65 82.19 124655 6334 88.07 0.2442 0.243 0.2463 0.2679 0.2713 RANDOM 13.233
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] -8.52 3.33 3.63 -2.73 0.71 11.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.614 r_dihedral_angle_4_deg 18.815 r_dihedral_angle_3_deg 17.182 r_dihedral_angle_1_deg 6.375 r_angle_refined_deg 1.622 r_angle_other_deg 1.299 r_chiral_restr 0.071 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.614 r_dihedral_angle_4_deg 18.815 r_dihedral_angle_3_deg 17.182 r_dihedral_angle_1_deg 6.375 r_angle_refined_deg 1.622 r_angle_other_deg 1.299 r_chiral_restr 0.071 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37771 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 79
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