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Structure of the antibacterial peptide ABC transporter McjD in a high energy outward occluded intermediate state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PL0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 10% PEG 4000, 0.1 M ammonium sulphate, 100 mM HEPES pH 7.5 and 22% glycerol
Crystal Properties Matthews coefficient Solvent content 5.33 76.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 235.29 α = 90 b = 105.04 β = 105.55 c = 117.37 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 60 PIXEL DECTRIS PILATUS 12M 2016-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I23 2.26 Diamond I23
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.4 95.3 94.2 0.055 0.99 18.1 6.4 22352 98.36
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.46 87.2 0.635 0.86 2.6 6.5
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 4pl0 3.4 95.3 22350 1068 58.6 0.257 0.257 0.2763 0.26 0.2792 RANDOM 108.59
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] 0.9021 -14.0367 3.6782 -4.5803
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.5 t_omega_torsion 2.48 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 3.5 t_omega_torsion 2.48 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 9095 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 66
Software Software Software Name Purpose BUSTER refinement XDS data reduction autoPROC data scaling PHASER phasing