☰ Navigation Tabs
Crystal structure of P.aeruginosa LpxC in complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UHM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 293 0.03M Diethylene glycol
0.03M Triethylene glycol
0.03M Tetraethylene glycol
0.03M Pentaethylene glycol
0.1M Tris - BICINE pH 8.5
20 % v/v PEG 500 MME
10 % w/v PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.28 46.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.716 α = 90 b = 67.046 β = 90.96 c = 63.258 γ = 90
Symmetry Space Group P 1 21 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 200K 2020-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54056
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 22.17 99.9 0.194 5.92 4.7 17500
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 100 0.561 1.67 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3UHM 2.1 22.17 16517 957 99.79 0.19689 0.19388 0.24964 0.231 RANDOM 23.751
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] 0.06 0.01 -0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.241 r_dihedral_angle_3_deg 15.383 r_dihedral_angle_4_deg 15.354 r_dihedral_angle_1_deg 7.508 r_long_range_B_refined 7.069 r_long_range_B_other 7.067 r_scangle_other 3.757 r_mcangle_it 2.929 r_mcangle_other 2.928 r_scbond_it 2.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.241 r_dihedral_angle_3_deg 15.383 r_dihedral_angle_4_deg 15.354 r_dihedral_angle_1_deg 7.508 r_long_range_B_refined 7.069 r_long_range_B_other 7.067 r_scangle_other 3.757 r_mcangle_it 2.929 r_mcangle_other 2.928 r_scbond_it 2.316 r_scbond_other 2.315 r_mcbond_it 1.828 r_mcbond_other 1.827 r_angle_refined_deg 1.663 r_angle_other_deg 1.339 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 2301 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing