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Structure of the ExbB/ExbD hexameric complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5SV0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 0.1 M glycine, pH 9.0, 0.15 M CaCl2, 40 % PEG 350 MME, 0.05-0.2 M L-arginine
Crystal Properties Matthews coefficient Solvent content 3.1 60.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.47 α = 90 b = 106.34 β = 111.75 c = 163.36 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 90 PIXEL DECTRIS PILATUS3 6M 2016-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.84 50.18 99.3 0.11 0.155 0.992 6.67 5 90711 53.73
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.84 2.94 0.5 0.706 0.751
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5SV0 2.84 50.18 90711 4546 99.3 0.247 0.245 0.288 0.2698 RANDOM 43.59
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] 12.1241 -1.6974 -7.9771 -4.147
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.25 t_omega_torsion 2.19 t_angle_deg 1.11 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.25 t_omega_torsion 2.19 t_angle_deg 1.11 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 19884 Nucleic Acid Atoms Solvent Atoms 769 Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement XDS data reduction XDS data scaling PHASER phasing