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Crystal structure of beta-glycosides-binding protein (W41A) of ABC transporter in an open state (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 2.09 41.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.35 α = 90 b = 63.25 β = 90 c = 103.95 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 2019-08-21 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 1.7 54.03 97.2 0.074 0.079 0.026 0.997 21.3 8.9 41739
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 1.7 1.73 94.3 0.35 0.372 0.126 0.939 8.4
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 1.7 54.03 39504 2102 96.6 0.1743 0.1723 0.183 0.2108 0.2199 RANDOM 20.702
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] -0.55 -2.77 3.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.578 r_dihedral_angle_4_deg 17.326 r_dihedral_angle_3_deg 14.549 r_dihedral_angle_1_deg 6.712 r_angle_refined_deg 2.128 r_angle_other_deg 1.616 r_chiral_restr 0.125 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.578 r_dihedral_angle_4_deg 17.326 r_dihedral_angle_3_deg 14.549 r_dihedral_angle_1_deg 6.712 r_angle_refined_deg 2.128 r_angle_other_deg 1.616 r_chiral_restr 0.125 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3185 Nucleic Acid Atoms Solvent Atoms 396 Heterogen Atoms 23
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