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Crystal Structure of the PBP/SBP MotA in complex with glucopinic acid from A. tumefaciens B6/R10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5L9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 PEG 4K, 100 mM Tris HCl, 200 mM CaCl2
Crystal Properties Matthews coefficient Solvent content 2.07 40.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.63 α = 90 b = 131.93 β = 91.71 c = 70.38 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2018-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 48.12 99.5 0.084 0.034 0.999 12.42 6.9 106626
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.96 1.143 0.462 0.699
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 5L9G 1.85 48.12 106623 5332 99.5 0.18 0.179 0.1858 0.199 0.2128 RANDOM 45.39
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] -5.2824 2.7168 8.2602 -2.9778
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.1 t_omega_torsion 3.31 t_angle_deg 1 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.1 t_omega_torsion 3.31 t_angle_deg 1 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10008 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 92
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing