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Structure of the antibacterial peptide ABC transporter McjD, solved at wavelength 2.75 A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 10% PEG 4000, 0.1 M ammonium sulphate, 100 mM HEPES pH 7.5 and 22% glycerol
Crystal Properties Matthews coefficient Solvent content 3.95 68.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.19 α = 90 b = 109.32 β = 90 c = 233.35 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 80 PIXEL DECTRIS PILATUS 12M 2017-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I23 2.7552 Diamond I23
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.8 54.67 96.8 0.2146 0.2167 0.02965 0.998 12.48 54.6 51873 83.08
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 0.675 0.27
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.8 54.67 49306 2578 99.74 0.29406 0.29209 0.297 0.32974 0.3296 RANDOM 163.335
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] 4.68 3.23 -7.91
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 18.144 r_long_range_B_other 18.144 r_dihedral_angle_3_deg 15.242 r_scangle_other 12.361 r_mcangle_it 11.399 r_mcangle_other 11.399 r_scbond_it 7.844 r_scbond_other 7.843 r_mcbond_it 7.555 r_mcbond_other 7.555
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 18.144 r_long_range_B_other 18.144 r_dihedral_angle_3_deg 15.242 r_scangle_other 12.361 r_mcangle_it 11.399 r_mcangle_other 11.399 r_scbond_it 7.844 r_scbond_other 7.843 r_mcbond_it 7.555 r_mcbond_other 7.555 r_dihedral_angle_2_deg 5.145 r_dihedral_angle_1_deg 3.392 r_angle_refined_deg 1.547 r_angle_other_deg 0.789 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.005 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8913 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling HKL2Map phasing