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Crystal structure of the lipopolysaccharide assembly complex LptD-LptE from the Escherichia coli outer membrane
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Q35
Crystallization Crystal Properties Matthews coefficient Solvent content 2.61 52.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.04 α = 90 b = 136.62 β = 90 c = 108.31 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray PIXEL PSI PILATUS 6M 2013-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979200 APS 24-ID-E
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 3.355 200 96.3 27863 26835 0.47
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 4Q35 3.355 108.31 25585 1250 96.31 0.2606 0.25668 0.2578 0.3378 0.3317 RANDOM 115.877
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] 3.97 1.34 -5.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.135 r_dihedral_angle_3_deg 19.812 r_long_range_B_refined 18.889 r_long_range_B_other 18.889 r_dihedral_angle_4_deg 16.951 r_mcangle_other 13.76 r_mcangle_it 13.216 r_scangle_other 12.994 r_dihedral_angle_1_deg 9.679 r_mcbond_it 8.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.135 r_dihedral_angle_3_deg 19.812 r_long_range_B_refined 18.889 r_long_range_B_other 18.889 r_dihedral_angle_4_deg 16.951 r_mcangle_other 13.76 r_mcangle_it 13.216 r_scangle_other 12.994 r_dihedral_angle_1_deg 9.679 r_mcbond_it 8.289 r_mcbond_other 8.289 r_scbond_other 8.018 r_scbond_it 7.649 r_angle_refined_deg 1.437 r_angle_other_deg 0.913 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 11498 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement