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Crystal structure of ABC transporter alpha-glycoside-binding protein in complex with maltose
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 2.9 57.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.24 α = 90 b = 85.24 β = 90 c = 145.68 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 2017-06-27 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 1.63 73.57 100 0.067 0.075 0.033 0.998 18.5 9 67774
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 1.63 8.92 99.9 0.242 0.278 0.135 0.97 5.5 8
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 1.63 73.57 64405 3303 99.95 0.1382 0.1369 0.137 0.1627 0.1627 RANDOM 17.239
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] 0.11 0.11 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.782 r_dihedral_angle_4_deg 15.746 r_dihedral_angle_3_deg 12.599 r_dihedral_angle_1_deg 5.782 r_angle_refined_deg 2.057 r_angle_other_deg 0.979 r_chiral_restr 0.138 r_bond_refined_d 0.022 r_gen_planes_refined 0.013 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.782 r_dihedral_angle_4_deg 15.746 r_dihedral_angle_3_deg 12.599 r_dihedral_angle_1_deg 5.782 r_angle_refined_deg 2.057 r_angle_other_deg 0.979 r_chiral_restr 0.138 r_bond_refined_d 0.022 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 3227 Nucleic Acid Atoms Solvent Atoms 575 Heterogen Atoms 44
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