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Crystal structure of E. coli LpxH in complex with lipid X
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other unpublished model from this lab
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 Morpheus III (G7)
1.2 % Cholic acid derivatives mix
0.1 M Buffer System 2 7.5
50 % Precipitant Mix 3
Crystal Properties Matthews coefficient Solvent content 2.97 58.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.827 α = 90 b = 81.392 β = 100.32 c = 33.127 γ = 90
Symmetry Space Group C 1 2 1
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 PILATUS 6M-F quasi-periodic elliptically polarizing undulator (qEPU) 2019-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91589 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.35 67.6 99 0.999 11.1 6.1 70366
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 1.35 1.42 0.827
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 MOLECULAR REPLACEMENT THROUGHOUT 1.35 30 66887 3468 99.17 0.17224 0.17146 0.1801 0.18733 0.193 RANDOM 16.599
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] 0.16 -1.4 1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.817 r_dihedral_angle_2_deg 7.337 r_dihedral_angle_1_deg 5.782 r_long_range_B_refined 4.327 r_long_range_B_other 4.139 r_scangle_other 2.933 r_scbond_it 1.968 r_scbond_other 1.945 r_mcangle_it 1.837 r_mcangle_other 1.837
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.817 r_dihedral_angle_2_deg 7.337 r_dihedral_angle_1_deg 5.782 r_long_range_B_refined 4.327 r_long_range_B_other 4.139 r_scangle_other 2.933 r_scbond_it 1.968 r_scbond_other 1.945 r_mcangle_it 1.837 r_mcangle_other 1.837 r_angle_refined_deg 1.281 r_mcbond_it 1.19 r_mcbond_other 1.173 r_angle_other_deg 0.465 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1901 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction SCALA data scaling PHASER phasing