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Structure of E. coli LpxH in complex with JEDI-1444
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other unpublished model from this lab
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 Morpheus III - G9
1.2 % Cholic acid derivatives mix 0.1 M
Buffer System 2 7.5
Precipitant Mix 1
Crystal Properties Matthews coefficient Solvent content 2.86 56.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.309 α = 90 b = 81.178 β = 103.32 c = 32.974 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 EIGER X 16M 2019-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.918401 MAX IV BioMAX
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 1.9 67 99.4 0.999 11.1 7.1 24774
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 1.9 2 0.814
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 1.9 50.01 23478 1293 99.98 0.17949 0.17771 0.1879 0.21174 0.2195 RANDOM 38.524
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] 1.75 1.66 -3.71 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.74 r_dihedral_angle_2_deg 9.22 r_long_range_B_refined 7.732 r_long_range_B_other 7.697 r_dihedral_angle_1_deg 6.957 r_scangle_other 5.896 r_mcangle_it 4.467 r_mcangle_other 4.467 r_scbond_it 4.165 r_scbond_other 4.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.74 r_dihedral_angle_2_deg 9.22 r_long_range_B_refined 7.732 r_long_range_B_other 7.697 r_dihedral_angle_1_deg 6.957 r_scangle_other 5.896 r_mcangle_it 4.467 r_mcangle_other 4.467 r_scbond_it 4.165 r_scbond_other 4.091 r_mcbond_it 3.36 r_mcbond_other 3.358 r_angle_refined_deg 1.527 r_angle_other_deg 0.5 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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 1826 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction SCALA data scaling PHASER phasing