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Crystal structure of lipopolysaccharide transport protein LptB in complex with ATP and Magnesium ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JI0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293.25 0.2M ammonium fluoride, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.25K
Crystal Properties Matthews coefficient Solvent content 2.17 43.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.16 α = 90 b = 125.76 β = 90 c = 89.61 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293.25 PIXEL DECTRIS PILATUS 6M mirros 2012-05-10 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) R Sym I (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 44.81 99.9 0.045 0.056 1 4.1 24034 24010 2 1.5 34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.22 2.29 99.9 0.57 0.6 2 4.3 2362
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1JI0 2.22 44.81 22834 22804 1230 99.42 0.185 0.18398 0.18067 0.1748 0.24825 0.2373 RANDOM 45.239
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] 9.13 3.49 -12.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.327 r_dihedral_angle_4_deg 20.728 r_dihedral_angle_3_deg 16.624 r_dihedral_angle_1_deg 6.343 r_angle_refined_deg 1.86 r_chiral_restr 0.125 r_bond_refined_d 0.016 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3658 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 64
Software Software Software Name Purpose DNA data collection MLPHARE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling