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Structure of K. pneumoniae LpxH in complex with JEDI-852
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other UNPUBLISHED MODEL FROM THIS LAB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 8.5 293 Morpheus III G12
1.2 % Cholic acid derivatives mix 0.1 M Buffer System 3 8.5
50 % Precipitant Mix 4
Crystal Properties Matthews coefficient Solvent content 2.63 53.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.013 α = 90 b = 60.013 β = 90 c = 284.658 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 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) 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 2 30 100 0.109 0.112 0.024 0.999 18.2 36 21782
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 0.752 0.771 0.177 0.98 5.4
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 29.38 20615 1054 99.92 0.22114 0.21902 0.2259 0.26351 0.2702 RANDOM 39.865
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] 0.48 0.24 0.48 -1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.107 r_long_range_B_other 8.269 r_long_range_B_refined 8.222 r_dihedral_angle_2_deg 7.76 r_dihedral_angle_1_deg 7.225 r_scangle_other 6.316 r_mcangle_it 5.169 r_mcangle_other 5.169 r_scbond_other 4.46 r_scbond_it 4.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.107 r_long_range_B_other 8.269 r_long_range_B_refined 8.222 r_dihedral_angle_2_deg 7.76 r_dihedral_angle_1_deg 7.225 r_scangle_other 6.316 r_mcangle_it 5.169 r_mcangle_other 5.169 r_scbond_other 4.46 r_scbond_it 4.44 r_mcbond_it 3.967 r_mcbond_other 3.965 r_angle_refined_deg 1.506 r_angle_other_deg 0.5 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 1836 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing