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Pseudomonas aeruginosa AchC1 (YfdX1) at pH 8.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.5 291 0.1 M (0.5 M Tris, 0.5 M bicine) buffer pH 8.5, 90 mM (0.3 M sodium nitrate, 0.3 M sodium phosphate dibasic, 0.3 M ammonium sulfate) additives, 0.12 M (0.3 M diethylene glycol, 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M pentaethylene glycol) ethyleneglycol and 37.5% (25% MPD, 25% PEG 1000, 25% PEG 3350) precipitant
Crystal Properties Matthews coefficient Solvent content 2.51 51.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.97 α = 90 b = 99.01 β = 90 c = 158.26 γ = 90
Symmetry Space Group I 2 2 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 EIGER X 9M 2023-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.92 29.38 99.5 0.99 17.68 13.64 47475 44.34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.98 98.86 0.636
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.92 29.38 1.34 47472 2374 99.55 0.2327 0.2315 0.2317 0.2542 0.2541 51.82
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.5656 f_angle_d 0.9223 f_chiral_restr 0.0524 f_plane_restr 0.0081 f_bond_d 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4026 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement autoPROC data processing Coot model building XSCALE data scaling PHASER phasing autoXDS data reduction