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Crystal structure of Pseudomonas aeruginosa LpxA in complex with compound 6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 278 1.5 M NH4Cl, 0.1 M Na Acetate pH 4.5
Crystal Properties Matthews coefficient Solvent content 4.05 69.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.392 α = 90 b = 166.392 β = 90 c = 99.501 γ = 90
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 2019-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 83.2 99.7 0.162 0.175 0.067 0.99 4.7 6.9 91413 32.87
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 2.03 93.4 1.356 1.467 0.557 0.665 6.9
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 5DEM 2 58.83 91289 4470 99.5 0.195 0.193 0.219 0.2353 RANDOM 48.35
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] 8.2308 8.2308 -16.4617
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.63 t_omega_torsion 3.52 t_angle_deg 1.08 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.63 t_omega_torsion 3.52 t_angle_deg 1.08 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5922 Nucleic Acid Atoms Solvent Atoms 516 Heterogen Atoms 98
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling MOLREP phasing