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Structure of the antibacterial peptide ABC transporter McjD in an apo inward occluded conformation
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, HANGING DROP 9 293 5 mM MgCl2, 24 % PEG400 and 100 mM glycine pH 9.0
Crystal Properties Matthews coefficient Solvent content 5.18 76.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.85 α = 90 b = 87.85 β = 90 c = 351.5 γ = 90
Symmetry Space Group P 42 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 60 CCD ADSC QUANTUM 315 2014-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
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 4.71 78.58 98.4 0.082 0.99 9.6 3.7 7675 260.22
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 4.71 4.83 94.4 0.145 0.65 1.4 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 4pl0 4.71 30.06 7623 376 98.27 0.3143 0.3133 0.3613 0.3344 0.3478 RANDOM 96.53
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] -44.5046 -44.5046 89.0092
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.86 t_omega_torsion 2.12 t_angle_deg 1.04 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 3.86 t_omega_torsion 2.12 t_angle_deg 1.04 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 4527 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement xia2 data reduction Aimless data scaling PHASER phasing MOLREP phasing