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Crystal structure of ABC transporter alpha-glycoside-binding protein in complex with palatinose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6J9W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5 277 0.05 M Citric Acid, 0.05 M Bis-Tris Propane, 16% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.87 57.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.77 α = 90 b = 84.77 β = 90 c = 145.83 γ = 90
Symmetry Space Group P 41 21 2
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 2018-02-27 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 1.9 73.29 99.9 0.083 0.097 0.05 0.997 13.2 6.6 42666
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 1.9 9.11 99.6 0.449 0.524 0.268 0.915 3.6 6.9
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 6J9W 1.9 73.29 40512 2097 99.9 0.1415 0.1394 0.1525 0.1816 0.1895 RANDOM 22.409
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] 0.84 0.84 -1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.738 r_dihedral_angle_4_deg 15.486 r_dihedral_angle_3_deg 13.363 r_dihedral_angle_1_deg 5.852 r_angle_refined_deg 1.804 r_angle_other_deg 0.902 r_chiral_restr 0.116 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.738 r_dihedral_angle_4_deg 15.486 r_dihedral_angle_3_deg 13.363 r_dihedral_angle_1_deg 5.852 r_angle_refined_deg 1.804 r_angle_other_deg 0.902 r_chiral_restr 0.116 r_bond_refined_d 0.018 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 3227 Nucleic Acid Atoms Solvent Atoms 517 Heterogen Atoms 49
Software Software Software Name Purpose HKL-3000 data collection iMOSFLM data reduction Aimless data scaling PHASER phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction