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Crystal structure of PA0012 complexed with cyclic-di-GMP from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold A0A6N0KW37
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293.15 5.3 mg/mL PA0012 and 2.5 mM cyclic-di-GMP. 0.2 M NH4SO4, 15% (w/v) PEG4000, 0.1 M Tri-NaCit pH=5.6
Crystal Properties Matthews coefficient Solvent content 2.88 57.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.317 α = 90 b = 50.317 β = 90 c = 90.596 γ = 90
Symmetry Space Group P 43 21 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 EIGER2 S 9M 2023-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0004 ALS 8.2.1
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 1.54 43.99 100 0.081 0.083 0.013 1 19 39.2 17945 23.1
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 1.54 1.57 99.9 1.064 1.08 0.187 0.971 32.9
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 (All) 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 1.541 43.988 17885 873 99.989 0.175 0.1733 0.1734 0.2101 0.2105 RANDOM 27.158
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] 0.631 0.631 -1.262
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.98 r_dihedral_angle_3_deg 10.457 r_lrange_other 6.977 r_lrange_it 6.971 r_dihedral_angle_1_deg 6.885 r_scangle_it 5.714 r_scangle_other 5.709 r_dihedral_angle_2_deg 4.335 r_mcangle_it 3.931 r_mcangle_other 3.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.98 r_dihedral_angle_3_deg 10.457 r_lrange_other 6.977 r_lrange_it 6.971 r_dihedral_angle_1_deg 6.885 r_scangle_it 5.714 r_scangle_other 5.709 r_dihedral_angle_2_deg 4.335 r_mcangle_it 3.931 r_mcangle_other 3.928 r_scbond_other 3.89 r_scbond_it 3.889 r_mcbond_it 2.629 r_mcbond_other 2.628 r_angle_refined_deg 2.048 r_angle_other_deg 0.744 r_dihedral_angle_other_2_deg 0.516 r_symmetry_nbd_refined 0.228 r_nbd_other 0.211 r_symmetry_nbd_other 0.195 r_nbd_refined 0.191 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.113 r_symmetry_nbtor_other 0.093 r_symmetry_xyhbond_nbd_refined 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 663 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction PHASER phasing Coot model building