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Crystal structure of ABC transporter alpha-glycoside-binding mutant protein W287A 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 6.4 277 0.04 M Citric Acid, 0.06 M Bis-Tris Propane, 16% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.83 56.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.1 α = 90 b = 84.1 β = 90 c = 146.02 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 2018-04-22 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 72.88 100 0.14 0.158 0.073 0.99 10.4 8.5 36237
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 8.94 100 0.574 0.653 0.308 0.917 3.4 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 6J9W 2 72.88 34304 1849 99.97 0.1525 0.1506 0.1616 0.1863 0.1944 RANDOM 22.99
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] 0.96 0.96 -1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.154 r_dihedral_angle_4_deg 15.827 r_dihedral_angle_3_deg 13.83 r_dihedral_angle_1_deg 5.887 r_angle_refined_deg 1.787 r_angle_other_deg 0.903 r_chiral_restr 0.104 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.154 r_dihedral_angle_4_deg 15.827 r_dihedral_angle_3_deg 13.83 r_dihedral_angle_1_deg 5.887 r_angle_refined_deg 1.787 r_angle_other_deg 0.903 r_chiral_restr 0.104 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3218 Nucleic Acid Atoms Solvent Atoms 448 Heterogen Atoms 48
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