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Structure of K.pneumoniae LpxH in complex with EBL-3218
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other An unpublished model from our lab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 6.5 293 1.2 % Cholic acid derivatives mix
0.1 M Buffer System 1 6.5
50 % Precipitant Mix 2
Crystal Properties Matthews coefficient Solvent content 2.71 54.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.604 α = 90 b = 60.604 β = 90 c = 287.228 γ = 120
Symmetry Space Group P 61 2 2
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 EIGER2 XE 16M 2020-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
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 2.2 30 100 0.999 21.6 20 17034
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 2.2 2.27 0.768
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 2.2 28.91 16103 831 99.91 0.23883 0.23565 0.2445 0.30274 0.2994 RANDOM 60.196
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] 0.94 0.47 0.94 -3.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.532 r_long_range_B_refined 8.479 r_long_range_B_other 8.312 r_dihedral_angle_2_deg 8.003 r_dihedral_angle_1_deg 7.454 r_mcangle_it 6.688 r_mcangle_other 6.687 r_scangle_other 6.529 r_mcbond_it 4.921 r_mcbond_other 4.921
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.532 r_long_range_B_refined 8.479 r_long_range_B_other 8.312 r_dihedral_angle_2_deg 8.003 r_dihedral_angle_1_deg 7.454 r_mcangle_it 6.688 r_mcangle_other 6.687 r_scangle_other 6.529 r_mcbond_it 4.921 r_mcbond_other 4.921 r_scbond_it 4.845 r_scbond_other 4.765 r_angle_refined_deg 1.273 r_angle_other_deg 0.452 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 1825 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing