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Crystal structure of apo-LptDE complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IVA 5IVA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 289 2% tacsimate (pH5.0), 16% PEG3350, 100mM sodium citrate tribasic dehydrate
Crystal Properties Matthews coefficient Solvent content 3.88 68.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.027 α = 90 b = 160.485 β = 90 c = 218.075 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 PILATUS3 6M 2016-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9792 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.2 50 96.5 0.674 0.742 0.38 5.2 5.4 65178 80.81
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.31 93.8 4.724 0.018 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5IVA 3.28 43.09 1.33 59016 2952 96.44 0.2439 0.2421 0.242 0.2788 0.2789 80.38
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.4865 f_angle_d 1.2123 f_chiral_restr 0.0598 f_bond_d 0.0162 f_plane_restr 0.0094
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15858 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing PHENIX refinement