☰ Navigation Tabs
Crystal Structure of LpxC from Pseudomonas aeruginosa complexed with the potent BB-78485 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P42 PDB ENTRY 1P42
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 PALPXC, 10 MG/ML IN 25 MM HEPES PH 7.0, 2 MM TCEP, 0.3 M NACL, 1MM ZNCL2. BB-78485 ADDED TO 1 MM. HANGING DROP, 0.1 M SODIUM CACODYLATE PH 6.5, 0.2 M AMMONIUM SULFATE AND 10 % PEG 8000, 10 MM ZNCL2.
Crystal Properties Matthews coefficient Solvent content 2.13 50.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.542 α = 90 b = 103.331 β = 90 c = 105.284 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 173 CCD ADSC CCD MIRRORS 2004-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID APS 17-ID
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 1.9 34.15 99.9 0.08 23.61 6.4 78112
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 1.9 1.97 99.5 0.52 2.5 5.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1P42 1.9 73.72 74089 3927 99.6 0.179 0.177 0.1934 0.221 0.2361 RANDOM 23.05
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] 0.75 -0.83 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.124 r_dihedral_angle_4_deg 15.259 r_dihedral_angle_3_deg 12.611 r_dihedral_angle_1_deg 5.822 r_scangle_it 1.856 r_scbond_it 1.289 r_angle_refined_deg 1.122 r_angle_other_deg 1.024 r_mcangle_it 0.768 r_mcbond_it 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.124 r_dihedral_angle_4_deg 15.259 r_dihedral_angle_3_deg 12.611 r_dihedral_angle_1_deg 5.822 r_scangle_it 1.856 r_scbond_it 1.289 r_angle_refined_deg 1.122 r_angle_other_deg 1.024 r_mcangle_it 0.768 r_mcbond_it 0.67 r_symmetry_vdw_other 0.262 r_nbd_refined 0.196 r_nbtor_refined 0.172 r_nbd_other 0.168 r_symmetry_vdw_refined 0.162 r_symmetry_hbond_refined 0.155 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.101 r_nbtor_other 0.079 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6863 Nucleic Acid Atoms Solvent Atoms 1223 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing