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Crystal structure of the outer membrane lipopolysaccharide transport protein LptE (RlpB) from Escherichia coli in the tetragonal crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NHR PDB ENTRY 4NHR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.8 M sodium formate, 0.1 M Tris/HOAc pH 8.50, 15% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.9 57.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.46 α = 90 b = 102.46 β = 90 c = 166.84 γ = 90
Symmetry Space Group P 41 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 DECTRIS PILATUS 6M 2011-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1 NSLS X25
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 2.2 200 100 45813 45803 1.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 99.9 1.57
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 PDB ENTRY 4NHR 2.2 87.31 43543 2260 99.97 0.22717 0.22536 0.2293 0.26176 0.2661 RANDOM 58.837
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] -0.83 -0.83 1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.641 r_dihedral_angle_4_deg 20.042 r_dihedral_angle_3_deg 18.416 r_long_range_B_other 12.868 r_long_range_B_refined 12.845 r_scangle_other 10.075 r_dihedral_angle_1_deg 8.151 r_mcangle_other 7.727 r_mcangle_it 7.479 r_scbond_it 6.855
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.641 r_dihedral_angle_4_deg 20.042 r_dihedral_angle_3_deg 18.416 r_long_range_B_other 12.868 r_long_range_B_refined 12.845 r_scangle_other 10.075 r_dihedral_angle_1_deg 8.151 r_mcangle_other 7.727 r_mcangle_it 7.479 r_scbond_it 6.855 r_scbond_other 6.844 r_mcbond_it 5.168 r_mcbond_other 5.168 r_angle_refined_deg 1.998 r_angle_other_deg 1.6 r_chiral_restr 0.123 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.008 r_gen_planes_other 0.006 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 4195 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 12
Software Software Software Name Purpose CBASS data collection PHASER phasing REFMAC refinement XDS data reduction Aimless data scaling