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(S)-4-Amino-5-phenoxypentanoate as a Selective Agonist of the Transcription Factor GabR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T4J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 10% PEG 3350, 100 mM imidazole pH 8.0, and 200 mM Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.44 49.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.65 α = 90 b = 152.65 β = 90 c = 69.16 γ = 90
Symmetry Space Group P 41 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 CCD ADSC QUANTUM 315r 2017-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9792 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.8 50 100 0.093 0.997 11.2 4.8 20715
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 2.8 2.95 0.998
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 4T4J 2.8 40 19629 1034 99.9 0.2023 0.1991 0.2631 0.2521 RANDOM 70.315
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] -0.59 -0.59 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.271 r_dihedral_angle_4_deg 20.529 r_dihedral_angle_3_deg 17.864 r_dihedral_angle_1_deg 7.156 r_angle_refined_deg 1.633 r_angle_other_deg 1.022 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.271 r_dihedral_angle_4_deg 20.529 r_dihedral_angle_3_deg 17.864 r_dihedral_angle_1_deg 7.156 r_angle_refined_deg 1.633 r_angle_other_deg 1.022 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5763 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 90
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing