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Crystal structure of a TetR family regulator AmvR from Acinetobacter Baumannii with spermidine bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8WP7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.02 M Sodium potassium phosphate pH 8.5
0.1 M Bis Tris Propane pH 8.5
20 % w/v PEG 3350
10 % v/v Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.31 46.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.84 α = 90 b = 65.52 β = 90 c = 100.89 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 100 PIXEL DECTRIS EIGER2 S 9M 2023-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979 SSRF BL02U1
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 1.46 40.42 99.5 0.997 9.1 3.7 13420
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 1.46 2.641 0.997
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 THROUGHOUT 2.55 29.92 1.35 13420 645 99.7 0.2302 0.2261 0.2307 0.3163 0.3215
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 4.08 f_angle_d 0.962 f_chiral_restr 0.049 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3006 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHASER phasing