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Crystal structure of the antibacterial peptide ABC transporter McjD in an outward occluded state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ONJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 293 100 mM sodium citrate pH 5.5, 45 mM NaCl and 26% PEG 400
Crystal Properties Matthews coefficient Solvent content 3.88 68.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.83 α = 90 b = 107.92 β = 90 c = 232.96 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2011-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.7 48.96 99.8 12.1 3.7 56627 69.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.78 99.6 1.5 3.8
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 2ONJ 2.7 48.96 56624 2891 99.66 0.2476 0.2466 0.2671 0.266 0.2896 RANDOM 99.23
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] -32.0258 -16.6587 48.6845
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.59 t_omega_torsion 2.46 t_angle_deg 1.05 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 3.59 t_omega_torsion 2.46 t_angle_deg 1.05 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 9109 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 106
Software Software Software Name Purpose BUSTER refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing