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Crystal structure of Escherichia coli LpxH in complex with EBL-2805
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other an unpublished model from our lab
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 3% w/v CHAPS,
3% w/v CHAPSO,
3% w/v Sodium glycocholate hydrate, 3% w/v Taurocholic acid sodium salt hydrate
Tris (base); BICINE, pH 8.5
40% v/v Ethylene glycol
20 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.02 59.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.563 α = 90 b = 52.271 β = 111.22 c = 86.355 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 2019-07-22 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 1.6 80.5 100 0.999 11.1 8.2 43761
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 1.6 1.63 0.753
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 1.6 80.5 41491 2269 99.96 0.18548 0.1844 0.195 0.20576 0.2181 RANDOM 15.317
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] 0.09 0.07 0.72 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.574 r_dihedral_angle_1_deg 5.985 r_dihedral_angle_2_deg 5.21 r_long_range_B_refined 3.786 r_long_range_B_other 3.585 r_scangle_other 1.929 r_mcangle_it 1.533 r_mcangle_other 1.533 r_scbond_it 1.199 r_scbond_other 1.195
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.574 r_dihedral_angle_1_deg 5.985 r_dihedral_angle_2_deg 5.21 r_long_range_B_refined 3.786 r_long_range_B_other 3.585 r_scangle_other 1.929 r_mcangle_it 1.533 r_mcangle_other 1.533 r_scbond_it 1.199 r_scbond_other 1.195 r_angle_refined_deg 1.041 r_mcbond_it 0.894 r_mcbond_other 0.894 r_angle_other_deg 0.382 r_chiral_restr 0.055 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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 1831 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing