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Crystal structure of type-I LOG from Pseudomonas aeruginosa PAO1 in complex with AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ITS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 293 ammonium phosphate dibasic, citrate pH 5.5, sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.6 52.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.844 α = 90 b = 97.524 β = 90 c = 71.788 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 270 2017-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 54 97.3 0.123 0.063 0.912 12.8 4.3 10160
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 2.3 2.34 0.349 0.162 0.713
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 5ITS 2.3 54 9646 505 97.11 0.1847 0.182 0.1882 0.2377 0.2307 RANDOM 16.208
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] -0.31 0.87 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.391 r_dihedral_angle_4_deg 20.551 r_dihedral_angle_3_deg 16.209 r_dihedral_angle_1_deg 5.854 r_angle_refined_deg 1.78 r_angle_other_deg 1.047 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.391 r_dihedral_angle_4_deg 20.551 r_dihedral_angle_3_deg 16.209 r_dihedral_angle_1_deg 5.854 r_angle_refined_deg 1.78 r_angle_other_deg 1.047 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1350 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling MOLREP phasing