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Structure of K.pneumoniae LpxH in complex with EBL-3339
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other unpublished model from this lab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 screen, G6
1.2 % Cholic acid derivatives mix 0.1 M Buffer System 2 7.5
50 % Precipitant Mix 2
Crystal Properties Matthews coefficient Solvent content 2.32 54.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.204 α = 90 b = 60.204 β = 90 c = 286.779 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 2020-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976254 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.95 30 88.5 0.09 0.094 0.028 0.999 20.5 20 21114 36.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 1.672 0.507 0.792
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 1.95 29.96 19918 1082 88.68 0.22506 0.22354 0.2318 0.25271 0.2584 RANDOM 39.787
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] 0.76 0.38 0.76 -2.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.705 r_dihedral_angle_1_deg 6.433 r_dihedral_angle_2_deg 6.38 r_long_range_B_refined 5.67 r_long_range_B_other 5.586 r_scangle_other 4.23 r_mcangle_it 3.776 r_mcangle_other 3.775 r_scbond_other 2.823 r_scbond_it 2.815
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.705 r_dihedral_angle_1_deg 6.433 r_dihedral_angle_2_deg 6.38 r_long_range_B_refined 5.67 r_long_range_B_other 5.586 r_scangle_other 4.23 r_mcangle_it 3.776 r_mcangle_other 3.775 r_scbond_other 2.823 r_scbond_it 2.815 r_mcbond_it 2.686 r_mcbond_other 2.686 r_angle_refined_deg 1.199 r_angle_other_deg 0.426 r_chiral_restr 0.065 r_bond_refined_d 0.007 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 1850 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling REFMAC phasing